updated avatar

Author: simongravelle

tutorial1/avatar/avatar.gro

@@ -2,7 +2,7 @@
 ;	File 'avatar.mdp' was generated
 ;	By user: simon (1000)
 ;	On host: laptop
-;	At date: Thu Apr 17 11:46:50 2025
+;	At date: Fri Apr 18 16:28:41 2025
 ;
 ;	Created by:
 ;	                     :-) GROMACS - gmx grompp, 2025.1 (-:
@@ -25,7 +25,7 @@ integrator               = md
 ; Start time and timestep in ps
 tinit                    = 0
 dt                       = 0.001
-nsteps                   = 4000
+nsteps                   = 2000
 ; For exact run continuation or redoing part of a run
 init-step                = 0
 ; Part index is updated automatically on checkpointing (keeps files separate)
@@ -71,7 +71,7 @@ nstlog                   = 100
 nstcalcenergy            = 100
 nstenergy                = 100
 ; Output frequency and precision for .xtc file
-nstxout-compressed       = 2
+nstxout-compressed       = 4
 compressed-x-precision   = 1000
 ; This selects the subset of atoms for the compressed
 ; trajectory file. You can select multiple groups. By
@@ -175,7 +175,7 @@ annealing-temp           =
 ; GENERATE VELOCITIES FOR STARTUP RUN
 gen-vel                  = no
 gen-temp                 = 300
-gen-seed                 = -675160514
+gen-seed                 = -1611165825
 
 ; OPTIONS FOR BONDS    
 constraints              = hbonds

tutorial1/avatar/avatar.mdp

@@ -276,7 +276,7 @@ atomselect macro qwikmd_hetero {(not name QWIKMDDELETE and hetero and not qwikmd
 # Display settings
 display eyesep       0.065000
 display focallength  2.000000
-display height       6.000000
+display height       1.000000
 display distance     -2.000000
 display projection   Orthographic
 display nearclip set 0.500000
@@ -300,13 +300,13 @@ mol addfile avatar.xtc type xtc first 0 last -1 step 1 filebonds 1 autobonds 1 w
 mol delrep 0 top
 mol representation VDW 0.900000 47.000000
 mol color Name
-mol selection {resid 2 14 18}
+mol selection {resid 2 18 }
 mol material Opaque
 mol addrep top
 mol selupdate 0 top 0
 mol colupdate 0 top 0
 mol scaleminmax top 0 0.000000 0.000000
-mol smoothrep top 0 0
+mol smoothrep top 0 1
 mol drawframes top 0 {now}
 mol clipplane center 0 0 top {0.0 0.0 0.0}
 mol clipplane color  0 0 top {0.5 0.5 0.5 }
@@ -332,15 +332,15 @@ mol clipplane center 5 0 top {0.0 0.0 0.0}
 mol clipplane color  5 0 top {0.5 0.5 0.5 }
 mol clipplane normal 5 0 top {0.0 0.0 1.0}
 mol clipplane status 5 0 top {0}
-mol representation DynamicBonds 1.600000 0.100000 42.000000
+mol representation DynamicBonds 1.300000 0.100000 42.000000
 mol color Name
-mol selection {type OW1 HW2 HW1 and same residue as (resname SOL and within 5 of resid 2 14 18)}
+mol selection {type OW1 HW2 HW1 and same residue as (resname SOL and within 5 of resid 2 18)}
 mol material Opaque
 mol addrep top
 mol selupdate 1 top 0
 mol colupdate 1 top 0
 mol scaleminmax top 1 0.000000 0.000000
-mol smoothrep top 1 0
+mol smoothrep top 1 1
 mol drawframes top 1 {now}
 mol clipplane center 0 1 top {0.0 0.0 0.0}
 mol clipplane color  0 1 top {0.5 0.5 0.5 }
@@ -374,7 +374,7 @@ mol addrep top
 mol selupdate 2 top 0
 mol colupdate 2 top 0
 mol scaleminmax top 2 0.000000 0.000000
-mol smoothrep top 2 0
+mol smoothrep top 2 1
 mol drawframes top 2 {now}
 mol clipplane center 0 2 top {0.0 0.0 0.0}
 mol clipplane color  0 2 top {0.5 0.5 0.5 }
@@ -400,11 +400,82 @@ mol clipplane center 5 2 top {0.0 0.0 0.0}
 mol clipplane color  5 2 top {0.5 0.5 0.5 }
 mol clipplane normal 5 2 top {0.0 0.0 1.0}
 mol clipplane status 5 2 top {0}
+mol showrep top 2 0
+mol representation VDW 0.900000 47.000000
+mol color Name
+mol selection {resname SO4 Na}
+mol material Opaque
+mol addrep top
+mol selupdate 3 top 0
+mol colupdate 3 top 0
+mol scaleminmax top 3 0.000000 0.000000
+mol smoothrep top 3 1
+mol drawframes top 3 {now}
+mol clipplane center 0 3 top {0.0 0.0 0.0}
+mol clipplane color  0 3 top {0.5 0.5 0.5 }
+mol clipplane normal 0 3 top {0.0 0.0 1.0}
+mol clipplane status 0 3 top {0}
+mol clipplane center 1 3 top {0.0 0.0 0.0}
+mol clipplane color  1 3 top {0.5 0.5 0.5 }
+mol clipplane normal 1 3 top {0.0 0.0 1.0}
+mol clipplane status 1 3 top {0}
+mol clipplane center 2 3 top {0.0 0.0 0.0}
+mol clipplane color  2 3 top {0.5 0.5 0.5 }
+mol clipplane normal 2 3 top {0.0 0.0 1.0}
+mol clipplane status 2 3 top {0}
+mol clipplane center 3 3 top {0.0 0.0 0.0}
+mol clipplane color  3 3 top {0.5 0.5 0.5 }
+mol clipplane normal 3 3 top {0.0 0.0 1.0}
+mol clipplane status 3 3 top {0}
+mol clipplane center 4 3 top {0.0 0.0 0.0}
+mol clipplane color  4 3 top {0.5 0.5 0.5 }
+mol clipplane normal 4 3 top {0.0 0.0 1.0}
+mol clipplane status 4 3 top {0}
+mol clipplane center 5 3 top {0.0 0.0 0.0}
+mol clipplane color  5 3 top {0.5 0.5 0.5 }
+mol clipplane normal 5 3 top {0.0 0.0 1.0}
+mol clipplane status 5 3 top {0}
+mol showrep top 3 0
+mol representation DynamicBonds 1.600000 0.100000 42.000000
+mol color Name
+mol selection {type OW1 HW2 HW1}
+mol material Opaque
+mol addrep top
+mol selupdate 4 top 0
+mol colupdate 4 top 0
+mol scaleminmax top 4 0.000000 0.000000
+mol smoothrep top 4 1
+mol drawframes top 4 {now}
+mol clipplane center 0 4 top {0.0 0.0 0.0}
+mol clipplane color  0 4 top {0.5 0.5 0.5 }
+mol clipplane normal 0 4 top {0.0 0.0 1.0}
+mol clipplane status 0 4 top {0}
+mol clipplane center 1 4 top {0.0 0.0 0.0}
+mol clipplane color  1 4 top {0.5 0.5 0.5 }
+mol clipplane normal 1 4 top {0.0 0.0 1.0}
+mol clipplane status 1 4 top {0}
+mol clipplane center 2 4 top {0.0 0.0 0.0}
+mol clipplane color  2 4 top {0.5 0.5 0.5 }
+mol clipplane normal 2 4 top {0.0 0.0 1.0}
+mol clipplane status 2 4 top {0}
+mol clipplane center 3 4 top {0.0 0.0 0.0}
+mol clipplane color  3 4 top {0.5 0.5 0.5 }
+mol clipplane normal 3 4 top {0.0 0.0 1.0}
+mol clipplane status 3 4 top {0}
+mol clipplane center 4 4 top {0.0 0.0 0.0}
+mol clipplane color  4 4 top {0.5 0.5 0.5 }
+mol clipplane normal 4 4 top {0.0 0.0 1.0}
+mol clipplane status 4 4 top {0}
+mol clipplane center 5 4 top {0.0 0.0 0.0}
+mol clipplane color  5 4 top {0.5 0.5 0.5 }
+mol clipplane normal 5 4 top {0.0 0.0 1.0}
+mol clipplane status 5 4 top {0}
+mol showrep top 4 0
 mol rename top avatar.gro
-set viewpoints([molinfo top]) {{{1 0 0 -14.8435} {0 1 0 -14.7803} {0 0 1 -14.6804} {0 0 0 1}} {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}} {{0.0704042 0 0 0} {0 0.0704042 0 0} {0 0 0.0704042 0} {0 0 0 1}} {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}}}
+set viewpoints([molinfo top]) {{{1 0 0 -22.1718} {0 1 0 -13.848} {0 0 1 -7.05399} {0 0 0 1}} {{0.969714 0.0937538 -0.225535 0} {-0.12632 0.982819 -0.134576 0} {0.209044 0.15899 0.964896 0} {0 0 0 1}} {{0.0258014 0 0 0} {0 0.0258014 0 0} {0 0 0.0258014 0} {0 0 0 1}} {{1 0 0 0.02} {0 1 0 0} {0 0 1 0} {0 0 0 1}}}
 lappend viewplist [molinfo top]
 set topmol [molinfo top]
-# done with molecule 1
+# done with molecule 0
 foreach v $viewplist {
   molinfo $v set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($v)
 }
@@ -574,7 +645,6 @@ color scale colors CET_R2 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
     {color Segname {} blue}
     {color Conformation {all} blue}
     {color Molecule {0} blue}
-    {color Molecule {1} red}
     {color Molecule {avatar.gro} red}
     {color Structure {3_10_Helix} blue}
     {color Surface {Grasp} gray}
@@ -593,7 +663,7 @@ color scale colors CET_R2 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
   color change rgb 6 0.6000000238418579 0.6000000238418579 0.6000000238418579
   color change rgb 7 0.0 1.0 0.0
   color change rgb 9 1.0 0.6000000238418579 0.6000000238418579
-  color change rgb 10 0.0 1.0 1.0
+  color change rgb 10 0.0 0.5273631811141968 0.5273631811141968
   color change rgb 11 0.6499999761581421 0.0 0.6499999761581421
   color change rgb 12 0.5 0.8999999761581421 0.4000000059604645
   color change rgb 13 0.8999999761581421 0.4000000059604645 0.699999988079071

tutorial1/avatar/avatar.vmd

@@ -0,0 +1,19 @@
+PATTERN    IBBPBBPBBPBBPBB
+FORCE_ENCODE_LAST_FRAME
+OUTPUT     /home/simon/Git/GROMACS/inputs/tutorial1/avatar/dark.mpg
+INPUT_DIR  /home/simon/Git/GROMACS/inputs/tutorial1/avatar
+INPUT
+dark.*.ppm [00000-00501]
+END_INPUT
+BASE_FILE_FORMAT PPM
+INPUT_CONVERT *
+GOP_SIZE 15
+SLICES_PER_FRAME 1
+PIXEL HALF
+RANGE 32
+PSEARCH_ALG LOGARITHMIC
+BSEARCH_ALG CROSS2
+IQSCALE 8
+PQSCALE 10
+BQSCALE 25
+REFERENCE_FRAME DECODED

tutorial1/avatar/dark.par

@@ -0,0 +1,45 @@
+#!/bin/bash
+set -e  # Stop on error
+
+# Function to process a sequence (dark or light)
+process_sequence() {
+    prefix="$1"
+
+    echo "Processing: $prefix"
+
+    # Convert PPM to PNG
+    for f in ${prefix}.*.ppm; do
+    convert "$f" "${f%.ppm}.png"
+    done
+
+    # Detect background color
+    bg_color="black"
+    if [[ "$prefix" == "light" ]]; then
+    bg_color="white"
+    fi
+
+    # Remove background & add alpha
+    for f in ${prefix}.*.png; do
+    convert "$f" -transparent "$bg_color" -fuzz 10% "${f%.png}_transparent.png"
+    done
+
+    # Resize
+    for f in ${prefix}.*_transparent.png; do
+    convert "$f" -resize 50% "$f"
+    done
+
+    # Create movie
+    [ -f "${prefix}.webp" ] && rm "${prefix}.webp"
+
+    ffmpeg -framerate 20 -i "${prefix}.%05d_transparent.png" \
+    -loop 0 -lossless 0 -qscale 5 -g 1 "${prefix}.webp"
+
+    # Cleanup PNGs
+    rm ${prefix}.*.png
+    convert ${prefix}.00000.ppm ${prefix}.png
+}
+
+# Run for both dark and light sequences
+process_sequence "dark"
+process_sequence "light"
+

tutorial1/avatar/dark.png

@@ -1,5 +1,5 @@
 integrator = md
-nsteps = 4000
+nsteps = 2000
 dt = 0.001
 
 comm_mode = linear
@@ -11,7 +11,7 @@ ns_type = grid
 
 nstlog = 100
 nstenergy = 100
-nstxout-compressed = 2
+nstxout-compressed = 4
 
 vdw-type = Cut-off
 rvdw = 1.0