Re: [gmx-users] using recolor.sh to color the xpm matrix files produced by r_rms and g_mdmat
Hi Hassan,
It seems the scripting language of the Gimp has changed a bit since
the version I used at the time of writing that script. The Gimp is
also only used for conversion of the xpm to png, which it did better
than convert. The important parts for recoloring are the lines using
convert, first generating a gradient, then applying that gradient on a
grayscale image. Try to find another way to convert xpm to png (or
another lossless format), and modify the script to your needs.
Cheers,
Tsjerk
On Thu, Dec 16, 2010 at 4:19 AM, Hassan Shallal hshal...@pacific.edu wrote:
Dear Gromacs users,
I have been trying to use the recolor.sh mentioned in this wbsite
http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html
http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html
to reclor an xpm file called rmsd-matrix.xpm file, whenever I issue the
command recolor.sh rmsd-matrix.xpm, I get the following error message:
#$ hassan~ $./recolor.sh rmsd-matrix.xpm
GIMP-Error: Opening '/home/hshallal/(gimp-file-save 1 1 2 ./rmsd-matrix.png
./rmsd-matrix.png)' failed: No such file or directory
GIMP-Error: Opening '/home/hshallal/(gimp-quit 0)' failed: No such file or
directory
batch command: executed successfully
It seems like a problem with gimp not being able to process as stated in the
script, especially with the argument of (gimp-file-save 1 1 2 \$png\
\$png\) (look below for the contents of the script).
I have gimp confidured in my system. has anyone ran across the same problem
or can know what the problem is and what th solution might be?
Thanks in advance
Hassan
The contents of the recolor.sh file:
#!/bin/sh
xpm=$1
png=`dirname $xpm`/`basename $xpm .xpm`.png
convert xc:red xc:orange xc:yellow xc:green1 xc:cyan xc:blue xc:magenta \
+append -filter Cubic -resize 600x30\! -rotate 90
gradient_rainbow.jpg
#convert -size 1x600 xc:'#0C0' -colorspace HSB \
# gradient: -compose CopyRed -composite \
# -colorspace RGB gradient_rainbow.jpg
gimp -d -f -i -b (gimp-file-load 1 \$xpm\ \$xpm\) (gimp-file-save 1 1
2 \$png\ \$png\) (gimp-quit 0)
convert $png gradient_rainbow.jpg -virtual-pixel edge -fx 'v.p{0,u*v.h}' $png
--
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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[gmx-users] different output generated by continue and discontinue simulation
Hi,
My gromacs version is 4.0.5.
I used grompp to generate tpr for 1ps simulation in this way
grompp -f md1.mdp -n index.ndx#160; -p topol.top -c 0ps.gro#160; -t 0ps.trr
-o 1ps.tpr
mdrun -s 1ps.tpr -e 1ps.edr -o 1ps.trr -g 1ps.log -c 1ps.gro
Here is my md1.mdp file:
;
title#160;#160;#160;#160;#160;#160;#160; = ttt
cpp#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; /lib/cpp
constraints#160;#160;#160;#160;#160;#160;#160;#160; =#160; hbonds
;define#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; -DFLEX_SPC
integrator#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; md
emtol#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 100.0
emstep#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.005
dt#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.002#160;#160;#160; ; ps !
nsteps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500#160; ; total 1 ps
nstcomm#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstxout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstvout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstfout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstlog#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstenergy#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160;
500
nstlist#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 5
ns_type#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; grid
rlist#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 1.
rcoulomb#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 1.
rvdw#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 1.
coulombtype#160;#160;#160;#160;#160;#160;#160;#160; =#160; PME
fourierspacing#160;#160;#160;#160;#160; =#160; 0.12
pme_order#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 4
optimize_fft#160;#160;#160;#160;#160;#160;#160; =#160; yes
Tcoupl#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; v-rescale
tc-grps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; A-chain B-chain drug SOL#160; NA+
;tau_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.1#160; 0.1
tau_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.2#160; 0.2 0.2 0.2 0.2
ref_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 300.00 300.00 300.00 300.00 300.00
energygrps#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160;
A-chain B-chain drug SOL#160; NA+
Pcoupl#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; berendsen
Pcoupltype#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160;
isotropic
;tau_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.1
tau_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.25
compressibility#160;#160;#160;#160; =#160; 5.4e-5
ref_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 1.0
gen_vel#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; yes
gen_temp#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 300.00
gen_seed#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 173531
--
Then I execute below loop in other 5 times for the totaly 60ns trajectories.
grompp -f md2.mdp -n index.ndx#160; -p topol.top -c ${n-1}ps.gro#160; -t
${n-1}ps.trr -o ${n}ps.tpr
mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c ${n}ps.gro
The file md2.mdp is almost the same as md1.mdp but the parameter gen_vel=no.
Here ${n-1}ps.gro and ${n-1}.trr mean I use last time frame trajectory to
continue.(I didn't really use this commend $(n-1) in bash script, it won't
work.)
I change the other way to run parallel simulation on the same system for double
check since above script is difficult to parallelize in public computer.
The new method is:
grompp -f md60ns.mdp -n index.ndx#160; -p topol.top -c 0ps.gro#160; -t
0ps.trr -o 60ns.tpr
mpiexec -np 8 mdrun_mpi -s 60ns.tpr -e 60ns.edr -o 60ns.trr -g 60ns.log -c
60ns.gro
The only different between md1.mdp and md60ns.mdp is nstep=3000 in
md60ns.mdp.
Theses two data generated by different ways are totaly different.
Here I mean different is not on the number buy mean the tendency of figure.
In the movie of first method, protein runs violently and go outside the
periodic boundary and then split by cubic edge.
The interaction energy within protein also fluctuate in an unstable way.
On the contrary, the second method generate a stable movie and fluctuation of
interaction energy.
Theotically these two should be the
[gmx-users] different output generated by continue and discontinue simulation
Sorry for the abnormal code.
I have fixed that.
---
Hi,
My gromacs version is 4.0.5.
I used grompp to generate tpr for 1ps simulation in this way
grompp -f md1.mdp -n index.ndx#160; -p topol.top -c 0ps.gro#160; -t 0ps.trr
-o 1ps.tpr
mdrun -s 1ps.tpr -e 1ps.edr -o 1ps.trr -g 1ps.log -c 1ps.gro
Here is my md1.mdp file:
;
title#160;#160;#160;#160;#160;#160;#160; = ttt
cpp#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; /lib/cpp
constraints#160;#160;#160;#160;#160;#160;#160;#160; =#160; hbonds
;define#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; -DFLEX_SPC
integrator#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; md
emtol#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 100.0
emstep#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.005
dt#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.002#160;#160;#160; ; ps !
nsteps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500#160; ; total 1 ps
nstcomm#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstxout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstvout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstfout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstlog#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 500
nstenergy#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160;
500
nstlist#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 5
ns_type#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; grid
rlist#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 1.
rcoulomb#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 1.
rvdw#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 1.
coulombtype#160;#160;#160;#160;#160;#160;#160;#160; =#160; PME
fourierspacing#160;#160;#160;#160;#160; =#160; 0.12
pme_order#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 4
optimize_fft#160;#160;#160;#160;#160;#160;#160; =#160; yes
Tcoupl#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; v-rescale
tc-grps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; A-chain B-chain drug SOL#160; NA+
;tau_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.1#160; 0.1
tau_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.2#160; 0.2 0.2 0.2 0.2
ref_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 300.00 300.00 300.00 300.00 300.00
energygrps#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160;
A-chain B-chain drug SOL#160; NA+
Pcoupl#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; berendsen
Pcoupltype#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160;
isotropic
;tau_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.1
tau_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 0.25
compressibility#160;#160;#160;#160; =#160; 5.4e-5
ref_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 1.0
gen_vel#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; yes
gen_temp#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 300.00
gen_seed#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 173531
--
Then I execute below loop in other 5 times for the totaly 60ns
trajectories.
grompp -f md2.mdp -n index.ndx#160; -p topol.top -c ${n-1}ps.gro#160; -t
${n-1}ps.trr -o ${n}ps.tpr
mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c ${n}ps.gro
The file md2.mdp is almost the same as md1.mdp but the parameter gen_vel=no.
Here ${n-1}ps.gro and ${n-1}.trr mean I use last time frame trajectory to
continue.(I didn't really use this commend $(n-1) in bash script, it won't
work.)
I change the other way to run parallel simulation on the same system fordouble
check since above script is difficult to parallelize in public computer.
The new method is:
grompp -f md60ns.mdp -n index.ndx#160; -p topol.top -c 0ps.gro#160; -t
0ps.trr -o 60ns.tpr
mpiexec -np 8 mdrun_mpi -s 60ns.tpr -e 60ns.edr -o 60ns.trr -g 60ns.log -c
60ns.gro
The only different between md1.mdp and md60ns.mdp is nstep=3000 in
md60ns.mdp.
Theses two data generated by different ways are totaly different.
Here I mean different is not on the number buy mean the tendency of figure.
In the movie of first method, protein runs violently and go outside the
periodic boundary and then split by cubic edge.
The interaction energy within protein also fluctuate in an unstable way.
On the contrary, the second
[gmx-users] water genbox 3x3x0.8 EM not successful T not high
Hi, I want to simulate 3x3x0.8 water film (bulk water) first creat the water, genbox -cs -o film.gro -box 3 3 0.8 then, i EM the bulk water; Using steep, but t = 0.011 ps: Water molecule starting at atom 298 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates then i run, and i get the result. I use NPT, and T=300K. I run several times, but the final T was still 411K. So what could i do to get EM process successful? And what is the reason ? why i can not control the T 300K? Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -9496.38136.145135.455 -0.158085 -47.4256 Kinetic En. 2358.273.587673.5471 -0.0281891 -8.45676 Total Energy -7138.19136.284135.326 -0.186274 -55.8824 Temperature 411.94512.854812.8477 -0.00492426 -1.47728 Pressure (bar) -1.66406704.355704.355 -0.00424907 -1.27473 Box-X 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Y 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Z 0.778108 0.00343907 0.00343437 -2.07536e-06 -0.000622609 Density (SI) 1038.713.616513.5998 0.007785132.33555 Heat Capacity Cv:12.49 J/mol K (factor = 0.000973754) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] different output generated by continue and discontinue simulation
Sorry for the abnormal code.
I have fixed that.
---
Hi,
My gromacs version is 4.0.5.
I used grompp to generate tpr for 1ps simulation in this way
grompp -f md1.mdp -n index.ndx#160; -p topol.top -c 0ps.gro#160; -t 0ps.trr
-o 1ps.tpr
mdrun -s 1ps.tpr -e 1ps.edr -o 1ps.trr -g 1ps.log -c 1ps.gro
Here is my md1.mdp file:
;
title = ttt
cpp = /lib/cpp #160;
constraints = hbons
;define = -DFLEX_SPC #160;
integrator = md#160;
emtol = 100.0
emstep = 0.005#160;
dt = 0.002 ; ps!
nsteps = 500 ; total 1ps
nstcomm = 500 #160;
ntsxout = 500 #160;
ntsvout = 500#160;
ntsfout = 500 #160;
ntslog = 500#160;
nstenergy = 500
nstlist = 5#160; #160;
ns_type = grid #160;
rlist = 1.
rcoulomb = 1.
rvdw = 1.
coulombtype = PME
fourierspacing = 0.12
pme_order = 4
optimize_fft = yes
Tcoupl = v-rescale
rc-grps = A-chain B-chain drug SOL NA+
;tau_t = 0.1 0.1
tau_t =0.2 0.2 0.2 0.2
ref_t = 300.00 300.00 300.00 300.0 300.00
energygrps = A-chain B-chain druhg SOL NA+
Pcoupl = berendsen
Pcoupltype = isotropic
;tau_p = 0.1
tau_p = 0.25
compressibility = 5.4e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 300.00
gen_seed = 173531
gen_seed#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 173531
--
Then I execute below loop in other 5 times for the totaly 60ns
trajectories.
grompp -f md2.mdp -n index.ndx#160; -p topol.top -c ${n-1}ps.gro#160; -t
${n-1}ps.trr -o ${n}ps.tpr
mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c ${n}ps.gro
The file md2.mdp is almost the same as md1.mdp but the parameter gen_vel=no.
Here ${n-1}ps.gro and ${n-1}.trr mean I use last time frame trajectory to
continue.(I didn't really use this commend $(n-1) in bash script, it won't
work.)
I change the other way to run parallel simulation on the same system fordouble
check since above script is difficult to parallelize in public computer.
The new method is:
grompp -f md60ns.mdp -n index.ndx#160; -p topol.top -c 0ps.gro#160; -t
0ps.trr -o 60ns.tpr
mpiexec -np 8 mdrun_mpi -s 60ns.tpr -e 60ns.edr -o 60ns.trr -g 60ns.log -c
60ns.gro
The only different between md1.mdp and md60ns.mdp is nstep=3000 in
md60ns.mdp.
Theses two data generated by different ways are totaly different.
Here I mean different is not on the number buy mean the tendency of figure.
In the movie of first method, protein runs violently and go outside the
periodic boundary and then split by cubic edge.
The interaction energy within protein also fluctuate in an unstable way.
On the contrary, the second method generate a stable movie and fluctuation of
interaction energy.
Theotically these two should be the same, right?
Is anything wrong in my work?
Sincerely yours,
Hsin-Lin
--- End of Forwarded Message ---
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
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Re: [gmx-users] water genbox 3x3x0.8 EM not successful T not high
Could you please attach your minimization parameters (mdp file) and grompp/mdrun commands? Your simulation box seems a bit strange for me. If you're using periodic boundary conditions you have not a thin film, but an infinite bulk water (remember pbc replicate the box in all directions). With such a small Z axis you might have probles with the cut-off radius being longer than a particle image. Javier El 16/12/10 10:38, gromacs escribió: Hi, I want to simulate 3x3x0.8 water film (bulk water) first creat the water, genbox -cs -o film.gro -box 3 3 0.8 then, i EM the bulk water; Using steep, but t = 0.011 ps: Water molecule starting at atom 298 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates then i run, and i get the result. I use NPT, and T=300K. I run several times, but the final T was still 411K. So what could i do to get EM process successful? And what is the reason ? why i can not control the T 300K? Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -9496.38 136.145 135.455 -0.158085 -47.4256 Kinetic En. 2358.2 73.5876 73.5471 -0.0281891 -8.45676 Total Energy -7138.19 136.284 135.326 -0.186274 -55.8824 Temperature 411.945 12.8548 12.8477 -0.00492426 -1.47728 Pressure (bar) -1.66406 704.355 704.355 -0.00424907 -1.27473 Box-X 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Y 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Z 0.778108 0.00343907 0.00343437 -2.07536e-06 -0.000622609 Density (SI)nbs p; 1038.7 13.6165 13.5998 0.00778513 2.33555 Heat Capacity Cv: 12.49 J/mol K (factor = 0.000973754) -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] water genbox 3x3x0.8 EM not successful T not high
On 12/16/10, Javier Cerezo j...@um.es wrote: Could you please attach your minimization parameters (mdp file) and grompp/mdrun commands? Your simulation box seems a bit strange for me. If you're using periodic boundary conditions you have not a thin film, but an infinite bulk water (remember pbc replicate the box in all directions). With such a small Z axis you might have probles with the cut-off radius being longer than a particle image. GROMACS enforces the minimum-image convention, so we can deduce that that rcoulomb was unreasonably short. El 16/12/10 10:38, gromacs escribió: Hi, I want to simulate 3x3x0.8 water film (bulk water) first creat the water, genbox -cs -o film.gro -box 3 3 0.8 then, i EM the bulk water; Using steep, but t = 0.011 ps: Water molecule starting at atom 298 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Here's the first hint something is wrong. Don't ignore it and plow on! then i run, and i get the result. I use NPT, and T=300K. I run several times, but the final T was still 411K. So what could i do to get EM process successful? And what is the reason ? why i can not control the T 300K? Over what timescale did you equilibrate? Over what *separate* timescale did you observe? Mark Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -9496.38 136.145 135.455 -0.158085 -47.4256 Kinetic En. 2358.2 73.5876 73.5471 -0.0281891 -8.45676 Total Energy -7138.19 136.284 135.326 -0.186274 -55.8824 Temperature 411.945 12.8548 12.8477 -0.00492426 -1.47728 Pressure (bar) -1.66406 704.355 704.355 -0.00424907 -1.27473 Box-X 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Y 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Z 0.778108 0.00343907 0.00343437 -2.07536e-06 -0.000622609 Density (SI)nbs p; 1038.7 13.6165 13.5998 0.00778513 2.33555 Heat Capacity Cv: 12.49 J/mol K (factor = 0.000973754) -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868887434 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] pullx.xvg / pullf.xvg
Hi, Following were the commands which i used in the umbrella sampling simulations: grompp -f md_umbrella.mdp -c conf500.gro -p topol.top -n index.ndx -o umbrella500.tpr mdrun -v -deffnm umbrella500 Output:umbrella500.xvg, umbrella500.xtc, umbrella500.trr, umbrella500.log, umbrella500.gro, umbrella500.edr, umbrella500.cpt pullf.xvg and pullx.xvg files were not produced. Please can I know should i mention -px pullx.xvg and -pf pullf.xvg in the mdrun? Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca] Sent: 15 December 2010 17:00 To: gmx-users@gromacs.org Subject: [gmx-users] pullx.xvg / pullf.xvg please copy and paste your commands your output. It is unlikely that any of us are going to do that tutorial in order to understand your question. -- original message -- Hi, I am following the umbrella sampling tutorial written by Justin Lemkul. I was successfully able to run the umbrella sampling simulations, but for each configuration it outputted a single xvg file. For the data analysis i should have pullf.xvg / pullx.xvg filesbut these files are not outputted after the simulation run. I haven't made any changes to the .mdp files mentioned in the tutorial. Please can i know what might have gone wrong that it has not produced pullf.xvg and pullx.xvg files. Kind regards, chetan. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pullx.xvg / pullf.xvg
On Dec 16, 2010, at 2:23 PM, Poojari, Chetan wrote: Hi, Following were the commands which i used in the umbrella sampling simulations: grompp -f md_umbrella.mdp -c conf500.gro -p topol.top -n index.ndx -o umbrella500.tpr mdrun -v -deffnm umbrella500 Output:umbrella500.xvg, umbrella500.xtc, umbrella500.trr, umbrella500.log, umbrella500.gro, umbrella500.edr, umbrella500.cpt pullf.xvg and pullx.xvg files were not produced. With -deffnm you specified a default filename for all output files. Try to use mdrun -pf pullf.xvg -px pullx.xvg -s input.tpr Adding -h to mdrun will show you how your output files will be called. Carsten Please can I know should i mention -px pullx.xvg and -pf pullf.xvg in the mdrun? Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca] Sent: 15 December 2010 17:00 To: gmx-users@gromacs.org Subject: [gmx-users] pullx.xvg / pullf.xvg please copy and paste your commands your output. It is unlikely that any of us are going to do that tutorial in order to understand your question. -- original message -- Hi, I am following the umbrella sampling tutorial written by Justin Lemkul. I was successfully able to run the umbrella sampling simulations, but for each configuration it outputted a single xvg file. For the data analysis i should have pullf.xvg / pullx.xvg filesbut these files are not outputted after the simulation run. I haven't made any changes to the .mdp files mentioned in the tutorial. Please can i know what might have gone wrong that it has not produced pullf.xvg and pullx.xvg files. Kind regards, chetan. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] pullx.xvg / pullf.xvg
Hi Carsten, Thank you very much. I reran my files: grompp -f md_umbrella.mdp -c conf144.gro -p topol.top -n index.ndx -o 144.tpr mdrun -s 144.tpr -rerun umbrella144.xtc -e 144.edr -o 144.trr -pf pullf.xvg -px pullx.xvg Output: 144.tpr, 144.trr, 144.edr, pullx.xvg, pullf.xvg. Kind regards, chetan. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Carsten Kutzner [ckut...@gwdg.de] Sent: 16 December 2010 14:28 To: Discussion list for GROMACS users Subject: Re: [gmx-users] pullx.xvg / pullf.xvg On Dec 16, 2010, at 2:23 PM, Poojari, Chetan wrote: Hi, Following were the commands which i used in the umbrella sampling simulations: grompp -f md_umbrella.mdp -c conf500.gro -p topol.top -n index.ndx -o umbrella500.tpr mdrun -v -deffnm umbrella500 Output:umbrella500.xvg, umbrella500.xtc, umbrella500.trr, umbrella500.log, umbrella500.gro, umbrella500.edr, umbrella500.cpt pullf.xvg and pullx.xvg files were not produced. With -deffnm you specified a default filename for all output files. Try to use mdrun -pf pullf.xvg -px pullx.xvg -s input.tpr Adding -h to mdrun will show you how your output files will be called. Carsten Please can I know should i mention -px pullx.xvg and -pf pullf.xvg in the mdrun? Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca] Sent: 15 December 2010 17:00 To: gmx-users@gromacs.org Subject: [gmx-users] pullx.xvg / pullf.xvg please copy and paste your commands your output. It is unlikely that any of us are going to do that tutorial in order to understand your question. -- original message -- Hi, I am following the umbrella sampling tutorial written by Justin Lemkul. I was successfully able to run the umbrella sampling simulations, but for each configuration it outputted a single xvg file. For the data analysis i should have pullf.xvg / pullx.xvg filesbut these files are not outputted after the simulation run. I haven't made any changes to the .mdp files mentioned in the tutorial. Please can i know what might have gone wrong that it has not produced pullf.xvg and pullx.xvg files. Kind regards, chetan. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] different output generated by continue and discontinue simulation
Hi, Mark
tc-grps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; A-chain B-chain drug SOL#160; NA+
This is bad - see http://www.gromacs.org/Documentation/Terminology/Thermostats
Thank you for your website.#160; I understand now.
grompp -f md2.mdp -n index.ndx#160; -p topol.top -c ${n-1}ps.gro#160; -t
${n-1}ps.trr -o ${n}ps.tpr
mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c ${n}ps.gro
You are following neither of the approaches recommended here
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
Ya, I'm sorry but my colleborator give me that before.
It is similiar to the commends connect position restrained dynamics and MD.
You can find grompp read gro and trr of last time frame to make a tpr file of
next time frame.
I thought this cause the time write on each snapshot is 0, but the dynamics is
still processing.
Did I miss something?
You say the pressure-coupling will be lost in each ps, does it mean that trr
file doesn't have this message inside?
Theses two data generated by different ways are totaly different.
Here I mean different is not on the number buy mean the tendency of figure.
See http://www.gromacs.org/Documentation/Terminology/Reproducibility
Ya, I know this since last time you show me this web in mailing list.
Thank you again.
But the different between these two outputs is totaly different.
I have four systems with different parameter gen_seed.
First is always unstable and irregular, but second is stable and regular.
On the contrary, the second method generate a stable movie and fluctuation
of interaction energy.
Theotically these two should be the same, right?
The second is probably happier about not losing the pressure-coupling
information every 1ns. However only much
much longer trajectories should show mutual convergence, and the movie is not
a reasonable way to look for it.
Mark
Sorry I don't understand you here.
Do you mean second way seems to more correct?
And what kind of mutual convergence you mean here?
Does It mean I can try to find mutual convergence in output of second way?
I'm sorry for my stupid and poor English.
Sincerely yours,
Hsin-Lin
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Re: [gmx-users] different output generated by continue and discontinue simulation
Hsin-Lin Chiang wrote:
Hi, Mark
tc-grps = A-chain B-chain drug SOL NA+
This is bad - see
http://www.gromacs.org/Documentation/Terminology/Thermostats
Thank you for your website. I understand now.
grompp -f md2.mdp -n index.ndx -p topol.top -c ${n-1}ps.gro -t
${n-1}ps.trr -o ${n}ps.tpr
mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c
${n}ps.gro
You are following neither of the approaches recommended here
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
Ya, I'm sorry but my colleborator give me that before.
It is similiar to the commends connect position restrained dynamics and MD.
You can find grompp read gro and trr of last time frame to make a tpr
file of next time frame.
I thought this cause the time write on each snapshot is 0, but the
dynamics is still processing.
Did I miss something?
You say the pressure-coupling will be lost in each ps, does it mean that
trr file doesn't have this message inside?
Pressure coupling information is stored in the .edr file. If you don't pass it
to grompp, you lose it. The better method is to use a checkpoint (.cpt) file,
which contains everything necessary to accurately continue the simulation.
Theses two data generated by different ways are totaly different.
Here I mean different is not on the number buy mean the tendency of
figure.
See http://www.gromacs.org/Documentation/Terminology/Reproducibility
Ya, I know this since last time you show me this web in mailing list.
Thank you again.
But the different between these two outputs is totaly different.
I have four systems with different parameter gen_seed.
First is always unstable and irregular, but second is stable and regular.
It sounds like you have an unstable system, that, under certain favorable
conditions, seems to work, but in other cases, doesn't. I'd investigate why the
first system is failing, since it probably really is a problem in all of them.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
On the contrary, the second method generate a stable movie and
fluctuation of interaction energy.
Theotically these two should be the same, right?
The second is probably happier about not losing the pressure-coupling
information every 1ns. However only much
much longer trajectories should show mutual convergence, and the
movie is not a reasonable way to look for it.
Mark
Sorry I don't understand you here.
Do you mean second way seems to more correct?
Not correct, but rather not yet suffering from the same problem.
And what kind of mutual convergence you mean here?
Systems only converge reliably over long time periods, i.e. in theory,
independent observations can only be reliably obtained over sufficient time.
-Justin
Does It mean I can try to find mutual convergence in output of second way?
I'm sorry for my stupid and poor English.
Sincerely yours,
Hsin-Lin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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[gmx-users] Brownian Dynamics Simulations generating huge log files
Hi, I am trying to simulate a system of 880 particles with implicit solvent using brownian dynamics, but the simulation generates huge log files (it writes md.log files at a rate of almost 5MB/minute) and this crashed my system since I ran out of space :( My mdp file looks like this: include = define = integrator = bd tinit= 0 dt = 0.001 nsteps = 1 ;10 simulation_part = 1 init_step= 0 comm-mode= Angular nstcomm = 1 comm-grps= emtol= 0.01 emstep = 1.5 nstxout = 1 nstvout = 1 nstfout = 1 nstenergy= 1000 nstxtcout= 1000 xtc-precision= 1000 nstlog = 0 xtc-grps = energygrps = ns_type = grid pbc = xyz periodic_molecules = no rlist= 8.95 coulombtype = user rcoulomb-switch = 0 rcoulomb = 8.95 epsilon-r= 1 vdw-type = user ;cutoff rvdw-switch = 0 rvdw = 8.95 DispCorr = No table-extension = 1 ; Seperate tables between energy group pairs energygrps = A T G C P300 SA SB energygrp_table = A A A T A G A C A P300 A SA A SB T T T G T C T P300 T SA T SB G G G C G P300 G SA G SB C C C P300 C SA C SB P300 P300 P 300 SA P300 SB SA SA SA SB SB SB ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.10 Tcoupl = Nose-Hoover tc-grps = System tau_t= 0.001 ref_t= 300.00 Pcoupl = No andersen_seed= 815131 gen_vel = yes gen_temp = 300. gen_seed = 1993 Please let me know if there is a solution to write smaller mdp files. I have set nstlog = 0 , but even that doesn't work! Thanks Nimesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Brownian Dynamics Simulations generating huge log files
Nimesh Jain wrote: Hi, I am trying to simulate a system of 880 particles with implicit solvent using brownian dynamics, but the simulation generates huge log files (it writes md.log files at a rate of almost 5MB/minute) and this crashed my system since I ran out of space :( My mdp file looks like this: include = define = integrator = bd tinit= 0 dt = 0.001 nsteps = 1 ;10 simulation_part = 1 init_step= 0 comm-mode= Angular nstcomm = 1 comm-grps= emtol= 0.01 emstep = 1.5 nstxout = 1 nstvout = 1 nstfout = 1 nstenergy= 1000 nstxtcout= 1000 xtc-precision= 1000 nstlog = 0 xtc-grps = energygrps = ns_type = grid pbc = xyz periodic_molecules = no rlist= 8.95 coulombtype = user rcoulomb-switch = 0 rcoulomb = 8.95 epsilon-r= 1 vdw-type = user ;cutoff rvdw-switch = 0 rvdw = 8.95 DispCorr = No table-extension = 1 ; Seperate tables between energy group pairs energygrps = A T G C P300 SA SB energygrp_table = A A A T A G A C A P300 A SA A SB T T T G T C T P300 T SA T SB G G G C G P300 G SA G SB C C C P300 C SA C SB P300 P300 P 300 SA P300 SB SA SA SA SB SB SB ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.10 Tcoupl = Nose-Hoover tc-grps = System tau_t= 0.001 This doesn't seem like a reasonable setting for tau_t; grompp should have warned you about that since dt = tau_t! ref_t= 300.00 Pcoupl = No andersen_seed= 815131 gen_vel = yes gen_temp = 300. gen_seed = 1993 Please let me know if there is a solution to write smaller mdp files. I have set nstlog = 0 , but even that doesn't work! Set nstlog to some incredibly large number, then, and it will only output a few times. It seems strange that nstlog = 0 didn't suppress the .log file output as it would any of the other nst* settings. -Justin Thanks Nimesh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: water genbox 3x3x0.8 EM not successful T not high
From: gromacs ptf1...@163.com Subject: [gmx-users] water genbox 3x3x0.8 EM not successful T not high Hi, I want to simulate 3x3x0.8 water film (bulk water) first creat the water, genbox -cs -o film.gro -box 3 3 0.8 then, i EM the bulk water; Using steep, but t = 0.011 ps: Water molecule starting at atom 298 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates then i run, and i get the result. I use NPT, and T=300K. I run several times, but the final T was still 411K. So what could i do to get EM process successful? And what is the reason ? why i can not control the T 300K? Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -9496.38 136.145 135.455 -0.158085 -47.4256 Kinetic En. 2358.2 73.5876 73.5471 -0.0281891 -8.45676 Total Energy -7138.19 136.284 135.326 -0.186274 -55.8824 Temperature 411.945 12.8548 12.8477 -0.00492426 -1.47728 Pressure (bar) -1.66406 704.355 704.355 -0.00424907 -1.27473 Box-X 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Y 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Z 0.778108 0.00343907 0.00343437 -2.07536e-06 -0.000622609 Density (SI) 1038.7 13.6165 13.5998 0.00778513 2.33555 Heat Capacity Cv: 12.49 J/mol K (factor = 0.000973754) Hey, gromacs - Nice to hear from you here... It is a bad idea to simulate something with any cartesian dimension lower than a couple of nanometers using classical FFs. All your problems are generated by 0.8 nm of the z-side. -- Dr. Vitaly V. Chaban Rochester, U.S.A. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Simulated Annealing parameters
Dear fellow GROMACS users, I am using the simulated annealing option in gromacs 4.5.2 (in an implicit solvent all-vs-all setting, by the way), i.e. using the annealing, annealing_npoints, annealing_time, annealing_temp parameters in the mdp file. I also specify the tcoupl, tc_grps and tau_t parameters for the temperature coupling, as well as the gen_vel, gen_temp, gen_seed ones for initial velocity generation. The perplexing behavior I'm encountering is that grompp requires me to specify also the ref_t parameter although it would seem to be overridden by the annealing parameters mentioned above. Am I doing anything wrong? If not, the correct behavior would be to warn when this parameter is specified rather than to demand it (and then presumably ignore it). Thanks in advance for your thoughts on the matter, Ehud Schreiber. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_bundle question
Hello, I am trying to calculate the tilt angle of the principal axis of a nanotube inserted into a membrane using g_bundle. In the index file I have selected a group of atoms at the top and a group of atoms at the bottom of the nanotube, and I using the option -na 1 and -z to calculate the tilt respect to the z axis of the membrane. I suppose that the results I have obtained in bun_tilt.xvg are the tilt angles respect to the average axis (along the simulation), is that right? Is there any way to calculate the tilt angle respect to a reference axis (for example, the axis formed by the 2 groups in the index file in the first structure, which is just perpendicular to the membrane? Thanks a lot in advance for your help. Best wishes, Rebeca Garcia Santiago de Compostela University Spain rega...@hotmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_bundle question
Rebeca García Fandiño wrote: Hello, I am trying to calculate the tilt angle of the principal axis of a nanotube inserted into a membrane using g_bundle. In the index file I have selected a group of atoms at the top and a group of atoms at the bottom of the nanotube, and I using the option -na 1 and -z to calculate the tilt respect to the z axis of the membrane. I suppose that the results I have obtained in bun_tilt.xvg are the tilt angles respect to the average axis (along the simulation), is that right? Is there any way to calculate the tilt angle respect to a reference axis (for example, the axis formed by the 2 groups in the index file in the first structure, which is just perpendicular to the membrane? Sounds like something g_sgangle can do. -Justin Thanks a lot in advance for your help. Best wishes, Rebeca Garcia Santiago de Compostela University Spain rega...@hotmail.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] tpr-files.dat and pullf-files.dat
Hi, I am doing data analysis of umbrella sampling tutorial. I have created 2 files : a) tpr-files.dat (under this folder i got ) 144.tpr 169.tpr 300.tpr 400.tpr 500.tpr b) pullf-files.dat pullf144.xvg pullf169.xvg pullf300.xvg pullf400.xvg pullf500.xvg When i run this command: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal I get the following error: Found 0 tpr and 0 pull force files in tpr-files.dat and pullf-files.dat, respectively Reading 0 tpr and pullf files. But both tpr-files.dat and pullf-files.dat contain all the .tpr and .xvg files· Please can someone suggest me how to go about this error message. Kind regards, chetan. Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Brownian Dynamics Simulations generating huge log files
Nimesh Jain wrote: I set nstlog = 1000, and still I get a 5MB log file within a minute of starting the sim. It seems absurd, but its happening :( Well, a log file will always be written with header information, etc, although 5 MB does seem quite large. The better question is whether or not it continues to get updated, causing the file size to increase. If it is, investigate what the contents are. Is the simulation crashing, causing thousands of lines of LINCS warnings to be printed? Is it normal output, but at a different frequency than what was specified? -Justin On Thu, Dec 16, 2010 at 10:05 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Nimesh Jain wrote: Hi, I am trying to simulate a system of 880 particles with implicit solvent using brownian dynamics, but the simulation generates huge log files (it writes md.log files at a rate of almost 5MB/minute) and this crashed my system since I ran out of space :( My mdp file looks like this: include = define = integrator = bd tinit= 0 dt = 0.001 nsteps = 1 ;10 simulation_part = 1 init_step= 0 comm-mode= Angular nstcomm = 1 comm-grps= emtol= 0.01 emstep = 1.5 nstxout = 1 nstvout = 1 nstfout = 1 nstenergy= 1000 nstxtcout= 1000 xtc-precision= 1000 nstlog = 0 xtc-grps = energygrps = ns_type = grid pbc = xyz periodic_molecules = no rlist= 8.95 coulombtype = user rcoulomb-switch = 0 rcoulomb = 8.95 epsilon-r= 1 vdw-type = user ;cutoff rvdw-switch = 0 rvdw = 8.95 DispCorr = No table-extension = 1 ; Seperate tables between energy group pairs energygrps = A T G C P300 SA SB energygrp_table = A A A T A G A C A P300 A SA A SB T T T G T C T P300 T SA T SB G G G C G P300 G SA G SB C C C P300 C SA C SB P300 P300 P 300 SA P300 SB SA SA SA SB SB SB ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.10 Tcoupl = Nose-Hoover tc-grps = System tau_t= 0.001 This doesn't seem like a reasonable setting for tau_t; grompp should have warned you about that since dt = tau_t! ref_t= 300.00 Pcoupl = No andersen_seed= 815131 gen_vel = yes gen_temp = 300. gen_seed = 1993 Please let me know if there is a solution to write smaller mdp files. I have set nstlog = 0 , but even that doesn't work! Set nstlog to some incredibly large number, then, and it will only output a few times. It seems strange that nstlog = 0 didn't suppress the .log file output as it would any of the other nst* settings. -Justin Thanks Nimesh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list
Re: [gmx-users] Brownian Dynamics Simulations generating huge log files
Nimesh Jain wrote: I am attaching the file, The simulation doesn't seem to crash, the log gets updated for sure. Hope you can make some sense of it. A few things: 1. Please do not attach entire log files. That took forever for my mail client to download with no ability to abort. http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette 2. Since I had already downloaded such an enormous file, I looked through it anyway, and found several potential problems: a. You probably have problems in your tables: WARNING: For the 4981 non-zero entries for table 2 in table_SA_SB.xvg the forces deviate on average 44% from minus the numerical derivative of the potential b. Your value of nstlog is nonsense: nstlog = 1215752192 indicates that mdrun did not find a reasonable value, i.e. you have exceeded the maximum size for an integer. Use a large, but sensible, setting. c. Your system is exploding, with a temperature of 1.14469e+04. I suspect that the large log file is produced by the instability of the system, and hence you're getting a huge amount of diagnostic information, much of which is somewhat cryptic. -Justin On Thu, Dec 16, 2010 at 1:50 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Nimesh Jain wrote: I set nstlog = 1000, and still I get a 5MB log file within a minute of starting the sim. It seems absurd, but its happening :( Well, a log file will always be written with header information, etc, although 5 MB does seem quite large. The better question is whether or not it continues to get updated, causing the file size to increase. If it is, investigate what the contents are. Is the simulation crashing, causing thousands of lines of LINCS warnings to be printed? Is it normal output, but at a different frequency than what was specified? -Justin On Thu, Dec 16, 2010 at 10:05 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Nimesh Jain wrote: Hi, I am trying to simulate a system of 880 particles with implicit solvent using brownian dynamics, but the simulation generates huge log files (it writes md.log files at a rate of almost 5MB/minute) and this crashed my system since I ran out of space :( My mdp file looks like this: include = define = integrator = bd tinit= 0 dt = 0.001 nsteps = 1 ;10 simulation_part = 1 init_step= 0 comm-mode= Angular nstcomm = 1 comm-grps= emtol= 0.01 emstep = 1.5 nstxout = 1 nstvout = 1 nstfout = 1 nstenergy= 1000 nstxtcout= 1000 xtc-precision= 1000 nstlog = 0 xtc-grps = energygrps = ns_type = grid pbc = xyz periodic_molecules = no rlist= 8.95 coulombtype = user rcoulomb-switch = 0 rcoulomb = 8.95 epsilon-r= 1 vdw-type = user ;cutoff rvdw-switch = 0 rvdw = 8.95 DispCorr = No table-extension = 1 ; Seperate tables between energy group pairs energygrps = A T G C P300 SA SB energygrp_table = A A A T A G A C A P300 A SA A SB T T T G T C T P300 T SA T SB G G G C G P300 G SA G SB C C C P300 C SA C SB P300 P300 P 300 SA P300 SB SA SA SA SB SB SB ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.10 Tcoupl = Nose-Hoover tc-grps = System tau_t= 0.001 This doesn't seem like a reasonable setting for tau_t; grompp should have warned you about that since dt = tau_t! ref_t= 300.00
RE: [gmx-users] tpr-files.dat and pullf-files.dat
Hello Justin, I had made mistake in creating the .dat files. I created just 5 windows between 0.2 to 5nm as i wanted to feel how things would work before setting up my system for umbrella sampling. And also to save up my computational time. So, After running the command: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal I get the below message. In the second line of the message it says Reading 2 tpr and pullf files...and as it can seen below it reads all the .tpr files. But it doesn't say anything about reading the .xvg files. Please can I know what exactly its doing here. Found 5 tpr and 5 pull force files in tpr-files.dat and pullf-files.dat, respectively Reading 2 tpr and pullf files Automatic determination of boundaries... Reading file 144.tpr, VERSION 4.0.7 (single precision) File 144.tpr, 1 groups, geometry distance, dimensions [N N Y], (1 dimensions) grp 0) k = 1000.000 inittial distance = 0.601453 Reading file 169.tpr, VERSION 4.0.7 (single precision) Reading file 300.tpr, VERSION 4.0.7 (single precision) Reading file 400.tpr, VERSION 4.0.7 (single precision) Reading file 500.tpr, VERSION 4.0.7 (single precision) Determined boundaries to 0.462181 and 5.585278 Reading file 144.tpr, VERSION 4.0.7 (single precision) Reading file 169.tpr, VERSION 4.0.7 (single precision) Reading file 300.tpr, VERSION 4.0.7 (single precision) Reading file 400.tpr, VERSION 4.0.7 (single precision) Reading file 500.tpr, VERSION 4.0.7 (single precision) Initialized rapid wham stuff. 1) Maximum change 5.326426e+00 Switched to exact iteration in iteration 44 Converged in 45 iterations. Final maximum change 6.37158e-07 Kind regards, chetan. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 16 December 2010 20:49 To: Discussion list for GROMACS users Subject: Re: [gmx-users] tpr-files.dat and pullf-files.dat Poojari, Chetan wrote: Hi, I am doing data analysis of umbrella sampling tutorial. I have created 2 files : a) tpr-files.dat (under this folder i got ) 144.tpr 169.tpr 300.tpr 400.tpr 500.tpr b) pullf-files.dat pullf144.xvg pullf169.xvg pullf300.xvg pullf400.xvg pullf500.xvg When i run this command: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal I get the following error: Found 0 tpr and 0 pull force files in tpr-files.dat and pullf-files.dat, respectively Reading 0 tpr and pullf files. But both tpr-files.dat and pullf-files.dat contain all the .tpr and .xvg files· Please can someone suggest me how to go about this error message. The only thing I can think of is incompatible line endings (i.e., Windows). Otherwise, plain text input is rather straightforward. -Justin Kind regards, chetan. Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] g_bundle question
Thanks for the suggestion. However, I have one question. If I use g_sgangle I can calculate the angle formed by the atoms at the top and bottom of my nanotube, but if the nanotube is considered as a whole (as a rigid system), and it tilts, then the result would not show the tilt respect to the z axis of the membrane, am I right? Thanks a lot for your help. Best wishes, Rebeca. Date: Thu, 16 Dec 2010 11:59:38 -0500 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] g_bundle question Rebeca García Fandiño wrote: Hello, I am trying to calculate the tilt angle of the principal axis of a nanotube inserted into a membrane using g_bundle. In the index file I have selected a group of atoms at the top and a group of atoms at the bottom of the nanotube, and I using the option -na 1 and -z to calculate the tilt respect to the z axis of the membrane. I suppose that the results I have obtained in bun_tilt.xvg are the tilt angles respect to the average axis (along the simulation), is that right? Is there any way to calculate the tilt angle respect to a reference axis (for example, the axis formed by the 2 groups in the index file in the first structure, which is just perpendicular to the membrane? Sounds like something g_sgangle can do. -Justin Thanks a lot in advance for your help. Best wishes, Rebeca Garcia Santiago de Compostela University Spain rega...@hotmail.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_bundle question
Rebeca García Fandiño wrote: Thanks for the suggestion. However, I have one question. If I use g_sgangle I can calculate the angle formed by the atoms at the top and bottom of my nanotube, but if the nanotube is considered as a whole (as a rigid system), and it tilts, then the result would not show the tilt respect to the z axis of the membrane, am I right? Maybe I'm not clear on what you want. I haven't used g_sgangle much, but it seems to me that option -oa (Angle between the two groups specified in the index file) would do what you want. Otherwise, g_sgangle -z might. -Justin Thanks a lot for your help. Best wishes, Rebeca. Date: Thu, 16 Dec 2010 11:59:38 -0500 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] g_bundle question Rebeca García Fandiño wrote: Hello, I am trying to calculate the tilt angle of the principal axis of a nanotube inserted into a membrane using g_bundle. In the index file I have selected a group of atoms at the top and a group of atoms at the bottom of the nanotube, and I using the option -na 1 and -z to calculate the tilt respect to the z axis of the membrane. I suppose that the results I have obtained in bun_tilt.xvg are the tilt angles respect to the average axis (along the simulation), is that right? Is there any way to calculate the tilt angle respect to a reference axis (for example, the axis formed by the 2 groups in the index file in the first structure, which is just perpendicular to the membrane? Sounds like something g_sgangle can do. -Justin Thanks a lot in advance for your help. Best wishes, Rebeca Garcia Santiago de Compostela University Spain rega...@hotmail.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] tpr-files.dat and pullf-files.dat
Poojari, Chetan wrote: Hello Justin, I had made mistake in creating the .dat files. I created just 5 windows between 0.2 to 5nm as i wanted to feel how things would work before setting up my system for umbrella sampling. And also to save up my computational time. So, After running the command: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal I get the below message. In the second line of the message it says Reading 2 tpr and pullf files...and as it can seen below it reads all the .tpr files. But it doesn't say anything about reading the .xvg files. Please can I know what exactly its doing here. Neither do I, but that's why the source code is available :) Presumably it's some sort of intermediate check. It looks like the rest of the process completed. The data are probably meaningless, though, so don't draw too much from it. Without sufficient window overlap, you'll have a poor PMF curve with lots of discontinuities. I suspect that five windows, spaced from 0.2 to 5 nm, will not really indicate if you've done anything correctly or not. -Justin Found 5 tpr and 5 pull force files in tpr-files.dat and pullf-files.dat, respectively Reading 2 tpr and pullf files Automatic determination of boundaries... Reading file 144.tpr, VERSION 4.0.7 (single precision) File 144.tpr, 1 groups, geometry distance, dimensions [N N Y], (1 dimensions) grp 0) k = 1000.000 inittial distance = 0.601453 Reading file 169.tpr, VERSION 4.0.7 (single precision) Reading file 300.tpr, VERSION 4.0.7 (single precision) Reading file 400.tpr, VERSION 4.0.7 (single precision) Reading file 500.tpr, VERSION 4.0.7 (single precision) Determined boundaries to 0.462181 and 5.585278 Reading file 144.tpr, VERSION 4.0.7 (single precision) Reading file 169.tpr, VERSION 4.0.7 (single precision) Reading file 300.tpr, VERSION 4.0.7 (single precision) Reading file 400.tpr, VERSION 4.0.7 (single precision) Reading file 500.tpr, VERSION 4.0.7 (single precision) Initialized rapid wham stuff. 1) Maximum change 5.326426e+00 Switched to exact iteration in iteration 44 Converged in 45 iterations. Final maximum change 6.37158e-07 Kind regards, chetan. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 16 December 2010 20:49 To: Discussion list for GROMACS users Subject: Re: [gmx-users] tpr-files.dat and pullf-files.dat Poojari, Chetan wrote: Hi, I am doing data analysis of umbrella sampling tutorial. I have created 2 files : a) tpr-files.dat (under this folder i got ) 144.tpr 169.tpr 300.tpr 400.tpr 500.tpr b) pullf-files.dat pullf144.xvg pullf169.xvg pullf300.xvg pullf400.xvg pullf500.xvg When i run this command: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal I get the following error: Found 0 tpr and 0 pull force files in tpr-files.dat and pullf-files.dat, respectively Reading 0 tpr and pullf files. But both tpr-files.dat and pullf-files.dat contain all the .tpr and .xvg files· Please can someone suggest me how to go about this error message. The only thing I can think of is incompatible line endings (i.e., Windows). Otherwise, plain text input is rather straightforward. -Justin Kind regards, chetan. Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA
RE: [gmx-users] g_bundle question
OK, you are right, I haven´t noticed the -z option! I will try it. Thanks a lot for your help. Best wishes, Rebeca. Date: Thu, 16 Dec 2010 15:34:05 -0500 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] g_bundle question Rebeca García Fandiño wrote: Thanks for the suggestion. However, I have one question. If I use g_sgangle I can calculate the angle formed by the atoms at the top and bottom of my nanotube, but if the nanotube is considered as a whole (as a rigid system), and it tilts, then the result would not show the tilt respect to the z axis of the membrane, am I right? Maybe I'm not clear on what you want. I haven't used g_sgangle much, but it seems to me that option -oa (Angle between the two groups specified in the index file) would do what you want. Otherwise, g_sgangle -z might. -Justin Thanks a lot for your help. Best wishes, Rebeca. Date: Thu, 16 Dec 2010 11:59:38 -0500 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] g_bundle question Rebeca García Fandiño wrote: Hello, I am trying to calculate the tilt angle of the principal axis of a nanotube inserted into a membrane using g_bundle. In the index file I have selected a group of atoms at the top and a group of atoms at the bottom of the nanotube, and I using the option -na 1 and -z to calculate the tilt respect to the z axis of the membrane. I suppose that the results I have obtained in bun_tilt.xvg are the tilt angles respect to the average axis (along the simulation), is that right? Is there any way to calculate the tilt angle respect to a reference axis (for example, the axis formed by the 2 groups in the index file in the first structure, which is just perpendicular to the membrane? Sounds like something g_sgangle can do. -Justin Thanks a lot in advance for your help. Best wishes, Rebeca Garcia Santiago de Compostela University Spain rega...@hotmail.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulated Annealing parameters
On 17/12/2010 3:38 AM, Ehud Schreiber wrote: Dear fellow GROMACS users, I am using the simulated annealing option in gromacs 4.5.2 (in an implicit solvent all-vs-all setting, by the way), i.e. using the annealing, annealing_npoints, annealing_time, annealing_temp parameters in the mdp file. I also specify the tcoupl, tc_grps and tau_t parameters for the temperature coupling, as well as the gen_vel, gen_temp, gen_seed ones for initial velocity generation. The perplexing behavior I'm encountering is that grompp requires me to specify also the ref_t parameter although it would seem to be overridden by the annealing parameters mentioned above. Am I doing anything wrong? If not, the correct behavior would be to warn when this parameter is specified rather than to demand it (and then presumably ignore it). It's easier to write and maintain code that functions the same way even when something is redundant in a particular case. Making the .mdp ref_t optional or illegal only when annealing is being used (when the SA implementation probably copies the SA values to the memory formerly occupied by the .mdp values) doesn't have enough of a gain to be worth the cost in coding time and ease of people understanding the full ramifications of the code. Thanks for the thought, though. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] water genbox 3x3x0.8 EM not successful T too high
Message: 3 Date: Thu, 16 Dec 2010 11:50:51 -0500 From: Vitaly Chaban vvcha...@gmail.com Subject: [gmx-users] Re: water genbox 3x3x0.8 EM not successful T not high To: gmx-users@gromacs.org Cc: gromacs ptf1...@163.com Message-ID: aanlktikykv=-oev10bxgys5n_nmqxbonwbhxkybuh...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 From: gromacs ptf1...@163.com Subject: [gmx-users] water genbox 3x3x0.8 EM not successful T not high Hi, I want to simulate 3x3x0.8 water film (bulk water) first creat the water, genbox -cs -o film.gro -box 3 3 0.8 then, i EM the bulk water; Using steep, but t = 0.011 ps: Water molecule starting at atom 298 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates then i run, and i get the result. I use NPT, and T=300K. I run several times, but the final T was still 411K. So what could i do to get EM process successful? And what is the reason ? why i can not control the T 300K? Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -9496.38136.145135.455 -0.158085 -47.4256 Kinetic En. 2358.273.587673.5471 -0.0281891 -8.45676 Total Energy -7138.19136.284135.326 -0.186274 -55.8824 Temperature 411.94512.854812.8477 -0.00492426 -1.47728 Pressure (bar) -1.66406704.355704.355 -0.00424907 -1.27473 Box-X 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Y 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Z 0.778108 0.00343907 0.00343437 -2.07536e-06 -0.000622609 Density (SI) 1038.713.616513.5998 0.00778513 2.33555 Heat Capacity Cv:12.49 J/mol K (factor = 0.000973754) Hey, gromacs - Nice to hear from you here... It is a bad idea to simulate something with any cartesian dimension lower than a couple of nanometers using classical FFs. All your problems are generated by 0.8 nm of the z-side. -- Dr. Vitaly V. Chaban Rochester, U.S.A. -- Thanks very much. I use the cutoff=0.38, because the cutoff should be smaller than the half box size. I guess it may be the Z dimension is too small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all results are OK. My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's rupture. So i have to run bulk 3x3x0.8 water and then add box to 3x3x9 to form interface. So if i want to run run bulk 3x3x0.8 water, how could i do? which FF should i use? the high T may be due to EM not success?? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] strange xpm output of g_rmsdist!
Thanks Tsjerk for the response. Just to follow on the thread for other users
who may get interested in recoloring matrix files, GUI of GIMP (newest version)
can allow recoloring any grayscale matrix file using several color gradient
maps already available within GIMP.
I have got another issue indeed to discuss with groamcs users, here is the
description:
Target: finding out the effect of a given mutation on the average distance
between the alpha carbon atom pairs in a given protein
Approach: after 20 ns simulation, g_rmsdist was used to derive the
2-dimensional matrix xpm for each system (mutant and wildtype) for comparison...
Problem: The xpm output for the wildtype system is very weird whereas the
output for the mutant one looks fine. In the weird xpm, there is just a white
diagonal line whereas everything else is black which means that the distances
between the alpha carbons exhibited massively big RMSD throughout the whole
trajectory. This is impossible, I checked the trajectory of that specific
system using VMD, it looks like any usual trajectory and the distances between
the alpha carbons were changing all the simulation time but the protein kept
its overall shape and secondary structure elements. Given this weird output
xpm, I would imagine that the protein completely unfolds!! So there must be
something wrong that happened while g_rmsdist was processing that specific
trajectory!!!
I plotted the corresponding xvg files (also generated by g_rmsdist). In both,
RMSD calculations looks fine and within acceptable range and upon plotting, the
RMSD curve of the mutant and that of the wildtpye were very close to each
others.
Here is the command I issued for checking:
g_rmsdist -s wildtype.tpr -f wildtype_noPBC_from_trr.xtc -o
wildtype_Calpha_rmsdist.xvg -rms wildtype_Calpha_rmsdist.xpm -scl
wildtype_Calpha_rmsscale.xpm -mean wildtype_Calpha_rmsmean.xpm
and exactly a similar one for the mutant system.
I am including a part of the content of both thw wildtype and the mutant xpm
for checking at the end of the message.. The numbers for color assignment in
the wildtype xpm are much much higher than those in the mutant one.
Question: has anyone encountered a similar problem with the g_rmsdist -rms xpm
output? is there any suggestion of what might have been wrong and what needs to
be corrected so that the g_rmsdist can give normal output for all the systems?
Any help would be greatly appreciated
Great regards
Hassan
A] wildtype_Calpha_rmsdist.xpm
/* XPM */
/* Generated by /home/hassan/bin/bin/g_rmsdist */
/* This file can be converted to EPS by the GROMACS program xpm2ps */
/* title: RMS of distance */
/* legend: RMS (nm) */
/* x-label: Atom Index */
/* y-label: Atom Index */
/* type:Continuous */
static char *gromacs_xpm[] = {
295 295 40 1,
A c #FF /* 0 */,
B c #F8F8F8 /* 7.7 */,
C c #F2F2F2 /* 15.4 */,
D c #EBEBEB /* 23.1 */,
E c #E5E5E5 /* 30.8 */,
F c #DEDEDE /* 38.5 */,
G c #D8D8D8 /* 46.2 */,
H c #D1D1D1 /* 53.9 */,
I c #CBCBCB /* 61.6 */,
J c #C4C4C4 /* 69.3 */,
K c #BEBEBE /* 77 */,
L c #B7B7B7 /* 84.7 */,
M c #B1B1B1 /* 92.5 */,
N c #AA /* 100 */,
O c #A3A3A3 /* 108 */,
P c #9D9D9D /* 116 */,
Q c #969696 /* 123 */,
R c #909090 /* 131 */,
S c #898989 /* 139 */,
T c #838383 /* 146 */,
U c #7C7C7C /* 154 */,
V c #767676 /* 162 */,
W c #6F6F6F /* 169 */,
X c #696969 /* 177 */,
Y c #626262 /* 185 */,
Z c #5C5C5C /* 193 */,
a c #55 /* 200 */,
b c #4E4E4E /* 208 */,
c c #484848 /* 216 */,
d c #414141 /* 223 */,
e c #3B3B3B /* 231 */,
f c #343434 /* 239 */,
g c #2E2E2E /* 247 */,
h c #272727 /* 254 */,
i c #212121 /* 262 */,
j c #1A1A1A /* 270 */,
k c #141414 /* 277 */,
l c #0D0D0D /* 285 */,
m c #070707 /* 293 */,
n c #00 /* 300 */,
/* x-axis: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51
52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77
78 79 80 */
/* x-axis: 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101
102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121
122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141
142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 */
/* x-axis: 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177
178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197
198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217
218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237
238 239 240 */
/* x-axis: 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257
258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277
278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295
[gmx-users] RE: pathologically expanding box
That did it, thanks Berk. On 12/15/10 1:13 AM, gmx-users-requ...@gromacs.org wrote: RE: pathologically expanding box -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] water genbox 3x3x0.8 EM not successful T too high
Why can't you energy minimise the water block / film in the final box size? And you can't simply change the cut-offs like that to suit your box size, you need to use the settings that the forcefield was parameterised for, or what others have studied / published and found to be suitable. You can't swap and changes those settings at a whim. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of gromacs Sent: Friday, 17 December 2010 11:32 AM To: gmx-users@gromacs.org Subject: [gmx-users] water genbox 3x3x0.8 EM not successful T too high Message: 3 Date: Thu, 16 Dec 2010 11:50:51 -0500 From: Vitaly Chaban vvcha...@gmail.com Subject: [gmx-users] Re: water genbox 3x3x0.8 EM not successful T not high To: gmx-users@gromacs.org Cc: gromacs ptf1...@163.com Message-ID: aanlktikykv=-oev10bxgys5n_nmqxbonwbhxkybuh...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 From: gromacs ptf1...@163.com Subject: [gmx-users] water genbox 3x3x0.8 EM not successful T not high Hi, I want to simulate 3x3x0.8 water film (bulk water) first creat the water, genbox -cs -o film.gro -box 3 3 0.8 then, i EM the bulk water; Using steep, but t = 0.011 ps: Water molecule starting at atom 298 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates then i run, and i get the result. I use NPT, and T=300K. I run several times, but the final T was still 411K. So what could i do to get EM process successful? And what is the reason ? why i can not control the T 300K? Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -9496.38136.145135.455 -0.158085 -47.4256 Kinetic En. 2358.273.587673.5471 -0.0281891 -8.45676 Total Energy -7138.19136.284135.326 -0.186274 -55.8824 Temperature 411.94512.854812.8477 -0.00492426 -1.47728 Pressure (bar) -1.66406704.355704.355 -0.00424907 -1.27473 Box-X 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Y 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Z 0.778108 0.00343907 0.00343437 -2.07536e-06 -0.000622609 Density (SI) 1038.713.616513.5998 0.00778513 2.33555 Heat Capacity Cv:12.49 J/mol K (factor = 0.000973754) Hey, gromacs - Nice to hear from you here... It is a bad idea to simulate something with any cartesian dimension lower than a couple of nanometers using classical FFs. All your problems are generated by 0.8 nm of the z-side. -- Dr. Vitaly V. Chaban Rochester, U.S.A. -- Thanks very much. I use the cutoff=0.38, because the cutoff should be smaller than the half box size. I guess it may be the Z dimension is too small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all results are OK. My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's rupture. So i have to run bulk 3x3x0.8 water and then add box to 3x3x9 to form interface. So if i want to run run bulk 3x3x0.8 water, how could i do? which FF should i use? the high T may be due to EM not success?? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re:Re: water genbox 3x3x0.8 EM not successful T not high
OK. I will use your method. But i am afraid there will be something wrong. Because generally, i should run the 3x3x0.8 NPT water, and then i use editconf to add the water to 3x3x3. If i donot run 3x3x0.8, i may not be able to run the final interface box. Because the water in the box is not at proper situation or position. Anyway, i will have a try first. If i have problem or success, i will give an answer to all. At 2010-12-17 09:51:57，Vitaly Chaban vvcha...@gmail.com wrote: Hey, gromacs - Nice to hear from you here... It is a bad idea to simulate something with any cartesian dimension lower than a couple of nanometers using classical FFs. All your problems are generated by 0.8 nm of the z-side. -- Dr. Vitaly V. Chaban Rochester, U.S.A. Thanks very much. I use the cutoff=0.38, because the cutoff should be smaller than the half box size. I guess it may be the Z dimension is too small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all results are OK. My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's rupture. So i have to run bulk 3x3x0.8 water and then add box to 3x3x9 to form interface. So if i want to run run bulk 3x3x0.8 water, how could i do? which FF should i use? the high T may be due to EM not success?? I believe you use the term bulk water in another sense as compared to all other guys here. When people say bulk liquid they imply the endless ocean of this liquid. It is not important what particular side lengths you have, since due to PBC you get infinitively large system. I suspect your teacher wants you to obtain a film of water that would be about 3 molecular layers wide. That's easy. Take your current box of water and apply editconf - editconf -f current_conf -o water_film_conf -box 3 3 3 Finally, just start MD run with a water_film_conf. You'll have the same periodic box , but water molecules will be present only at its center surrounded by vacuum in one (Z) direction. Happy GROMACSing, Dr. Vitaly V. Chaban Rochester, U.S.A. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] water genbox 3x3x0.8 EM not successful T not high
Forwarding messages From: gromacs ptf1...@163.com Date: 2010-12-17 12:48:55To: vvcha...@gmail.com Cc: gmx-users@gromacs.org Subject: Re:Re: water genbox 3x3x0.8 EM not successful T not high OK. I will use your method. But i am afraid there will be something wrong. Because generally, i should run the 3x3x0.8 NPT water, and then i use editconf to add the water to 3x3x3. If i donot run 3x3x0.8, i may not be able to run the final interface box. Because the water in the box is not at proper situation or position. Anyway, i will have a try first. One problem is that how can i make the Energy Minimising successful? There are some water molecules not in suitable position. If i have problem or success, i will give an answer to all. At 2010-12-17 09:51:57，Vitaly Chaban vvcha...@gmail.com wrote: Hey, gromacs - Nice to hear from you here... It is a bad idea to simulate something with any cartesian dimension lower than a couple of nanometers using classical FFs. All your problems are generated by 0.8 nm of the z-side.-- Dr. Vitaly V. Chaban Rochester, U.S.A. Thanks very much. I use the cutoff=0.38, because the cutoff should be smaller than the half box size. I guess it may be the Z dimension is too small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all results are OK. My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's rupture. So i have to run bulk 3x3x0.8 water and then add box to 3x3x9 to form interface. So if i want to run run bulk 3x3x0.8 water, how could i do? which FF should i use? the high T may be due to EM not success?? I believe you use the term bulk water in another sense as compared to all other guys here. When people say bulk liquid they imply the endless ocean of this liquid. It is not important what particular side lengths you have, since due to PBC you get infinitively large system. I suspect your teacher wants you to obtain a film of water that would be about 3 molecular layers wide. That's easy. Take your current box of water and apply editconf - editconf -f current_conf -o water_film_conf -box 3 3 3 Finally, just start MD run with a water_film_conf. You'll have the same periodic box , but water molecules will be present only at its center surrounded by vacuum in one (Z) direction. Happy GROMACSing,Dr. Vitaly V. Chaban Rochester, U.S.A.-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Re: water genbox 3x3x0.8 EM not successful T not high
I still do not understand what physical system you want to create in the MD system or what phenomenon you want to reproduce. If you need a water film, then the only solution is to follow my former suggestion. In no case should you use 3x3x0.8 NPT MD box! If somebody suggested you to do such thing, then this person simply does not understand classical MD simulations. -- Dr.Vitaly V. Chaban On Thu, Dec 16, 2010 at 11:48 PM, gromacs ptf1...@163.com wrote: OK. I will use your method. But i am afraid there will be something wrong. Because generally, i should run the 3x3x0.8 NPT water, and then i use editconf to add the water to 3x3x3. If i donot run 3x3x0.8, i may not be able to run the final interface box. Because the water in the box is not at proper situation or position. Anyway, i will have a try first. If i have problem or success, i will give an answer to all. At 2010-12-17 09:51:57，Vitaly Chaban vvcha...@gmail.com wrote: Hey, gromacs - Nice to hear from you here... It is a bad idea to simulate something with any cartesian dimension lower than a couple of nanometers using classical FFs. All your problems are generated by 0.8 nm of the z-side. -- Dr. Vitaly V. Chaban Rochester, U.S.A. Thanks very much. I use the cutoff=0.38, because the cutoff should be smaller than the half box size. I guess it may be the Z dimension is too small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all results are OK. My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's rupture. So i have to run bulk 3x3x0.8 water and then add box to 3x3x9 to form interface. So if i want to run run bulk 3x3x0.8 water, how could i do? which FF should i use? the high T may be due to EM not success?? I believe you use the term bulk water in another sense as compared to all other guys here. When people say bulk liquid they imply the endless ocean of this liquid. It is not important what particular side lengths you have, since due to PBC you get infinitively large system. I suspect your teacher wants you to obtain a film of water that would be about 3 molecular layers wide. That's easy. Take your current box of water and apply editconf - editconf -f current_conf -o water_film_conf -box 3 3 3 Finally, just start MD run with a water_film_conf. You'll have the same periodic box , but water molecules will be present only at its center surrounded by vacuum in one (Z) direction. Happy GROMACSing, Dr. Vitaly V. Chaban Rochester, U.S.A. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re:Re: Re: water genbox 3x3x0.8 EM not successful T not high
Yes. I should first run the 3x3x0.8 water to make the water inequilibrium. And then i use editconf to put the water at the centre of 3x3x9 box, so the film was 0.8 nm, the Z dimension is 9 nm, so there will be film. I want to simulate the rupture of the thickness of water film. If i directly put the 3x3x0.8 water in the 3x3x9 box, i will try to see the result. I At 2010-12-17 13:12:43，Vitaly Chaban vvcha...@gmail.com wrote: I still do not understand what physical system you want to create in the MD system or what phenomenon you want to reproduce. If you need a water film, then the only solution is to follow my former suggestion. In no case should you use 3x3x0.8 NPT MD box! If somebody suggested you to do such thing, then this person simply does not understand classical MD simulations. -- Dr.Vitaly V. Chaban On Thu, Dec 16, 2010 at 11:48 PM, gromacs ptf1...@163.com wrote: OK. I will use your method. But i am afraid there will be something wrong. Because generally, i should run the 3x3x0.8 NPT water, and then i use editconf to add the water to 3x3x3. If i donot run 3x3x0.8, i may not be able to run the final interface box. Because the water in the box is not at proper situation or position. Anyway, i will have a try first. If i have problem or success, i will give an answer to all. At 2010-12-17 09:51:57，Vitaly Chaban vvcha...@gmail.com wrote: Hey, gromacs - Nice to hear from you here... It is a bad idea to simulate something with any cartesian dimension lower than a couple of nanometers using classical FFs. All your problems are generated by 0.8 nm of the z-side. -- Dr. Vitaly V. Chaban Rochester, U.S.A. Thanks very much. I use the cutoff=0.38, because the cutoff should be smaller than the half box size. I guess it may be the Z dimension is too small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all results are OK. My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's rupture. So i have to run bulk 3x3x0.8 water and then add box to 3x3x9 to form interface. So if i want to run run bulk 3x3x0.8 water, how could i do? which FF should i use? the high T may be due to EM not success?? I believe you use the term bulk water in another sense as compared to all other guys here. When people say bulk liquid they imply the endless ocean of this liquid. It is not important what particular side lengths you have, since due to PBC you get infinitively large system. I suspect your teacher wants you to obtain a film of water that would be about 3 molecular layers wide. That's easy. Take your current box of water and apply editconf - editconf -f current_conf -o water_film_conf -box 3 3 3 Finally, just start MD run with a water_film_conf. You'll have the same periodic box , but water molecules will be present only at its center surrounded by vacuum in one (Z) direction. Happy GROMACSing, Dr. Vitaly V. Chaban Rochester, U.S.A. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Re: Re: water genbox 3x3x0.8 EM not successful T not high
You SHOULD bring water to EQUILIBRIUM starting from 3x3x9 box with water at the center of this box. You will NEVER get EQUILIBRIUM water film using 3x3x0.8. Yes. I should first run the 3x3x0.8 water to make the water in equilibrium. And then i use editconf to put the water at the centre of 3x3x9 box, so the film was 0.8 nm, the Z dimension is 9 nm, so there will be film. I want to simulate the rupture of the thickness of water film. If i directly put the 3x3x0.8 water in the 3x3x9 box, i will try to see the result. I At 2010-12-17 13:12:43，Vitaly Chaban vvcha...@gmail.com wrote: I still do not understand what physical system you want to create in the MD system or what phenomenon you want to reproduce. If you need a water film, then the only solution is to follow my former suggestion. In no case should you use 3x3x0.8 NPT MD box! If somebody suggested you to do such thing, then this person simply does not understand classical MD simulations. -- Dr.Vitaly V. Chaban On Thu, Dec 16, 2010 at 11:48 PM, gromacs ptf1...@163.com wrote: OK. I will use your method. But i am afraid there will be something wrong. Because generally, i should run the 3x3x0.8 NPT water, and then i use editconf to add the water to 3x3x3. If i donot run 3x3x0.8, i may not be able to run the final interface box. Because the water in the box is not at proper situation or position. Anyway, i will have a try first. If i have problem or success, i will give an answer to all. At 2010-12-17 09:51:57，Vitaly Chaban vvcha...@gmail.com wrote: Hey, gromacs - Nice to hear from you here... It is a bad idea to simulate something with any cartesian dimension lower than a couple of nanometers using classical FFs. All your problems are generated by 0.8 nm of the z-side. -- Dr. Vitaly V. Chaban Rochester, U.S.A. Thanks very much. I use the cutoff=0.38, because the cutoff should be smaller than the half box size. I guess it may be the Z dimension is too small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all results are OK. My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's rupture. So i have to run bulk 3x3x0.8 water and then add box to 3x3x9 to form interface. So if i want to run run bulk 3x3x0.8 water, how could i do? which FF should i use? the high T may be due to EM not success?? I believe you use the term bulk water in another sense as compared to all other guys here. When people say bulk liquid they imply the endless ocean of this liquid. It is not important what particular side lengths you have, since due to PBC you get infinitively large system. I suspect your teacher wants you to obtain a film of water that would be about 3 molecular layers wide. That's easy. Take your current box of water and apply editconf - editconf -f current_conf -o water_film_conf -box 3 3 3 Finally, just start MD run with a water_film_conf. You'll have the same periodic box , but water molecules will be present only at its center surrounded by vacuum in one (Z) direction. Happy GROMACSing, Dr. Vitaly V. Chaban Rochester, U.S.A. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Re: Re: water genbox 3x3x0.8 EM not successful T not high
Another issue that you will get in future. With such a system you should use NVT ensemble to maintain liquid-vapor interface in your system. Generally, NPT also can be used, but before you need run NVT anyway in order to create this liquid-vapor interface. Otherwise, the system will collapse at the first steps. Good luck. Dr. Vitaly V. Chaban On Fri, Dec 17, 2010 at 12:46 AM, Vitaly Chaban vvcha...@gmail.com wrote: You SHOULD bring water to EQUILIBRIUM starting from 3x3x9 box with water at the center of this box. You will NEVER get EQUILIBRIUM water film using 3x3x0.8. Yes. I should first run the 3x3x0.8 water to make the water in equilibrium. And then i use editconf to put the water at the centre of 3x3x9 box, so the film was 0.8 nm, the Z dimension is 9 nm, so there will be film. I want to simulate the rupture of the thickness of water film. If i directly put the 3x3x0.8 water in the 3x3x9 box, i will try to see the result. I At 2010-12-17 13:12:43，Vitaly Chaban vvcha...@gmail.com wrote: I still do not understand what physical system you want to create in the MD system or what phenomenon you want to reproduce. If you need a water film, then the only solution is to follow my former suggestion. In no case should you use 3x3x0.8 NPT MD box! If somebody suggested you to do such thing, then this person simply does not understand classical MD simulations. -- Dr.Vitaly V. Chaban On Thu, Dec 16, 2010 at 11:48 PM, gromacs ptf1...@163.com wrote: OK. I will use your method. But i am afraid there will be something wrong. Because generally, i should run the 3x3x0.8 NPT water, and then i use editconf to add the water to 3x3x3. If i donot run 3x3x0.8, i may not be able to run the final interface box. Because the water in the box is not at proper situation or position. Anyway, i will have a try first. If i have problem or success, i will give an answer to all. At 2010-12-17 09:51:57，Vitaly Chaban vvcha...@gmail.com wrote: Hey, gromacs - Nice to hear from you here... It is a bad idea to simulate something with any cartesian dimension lower than a couple of nanometers using classical FFs. All your problems are generated by 0.8 nm of the z-side. -- Dr. Vitaly V. Chaban Rochester, U.S.A. Thanks very much. I use the cutoff=0.38, because the cutoff should be smaller than the half box size. I guess it may be the Z dimension is too small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all results are OK. My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's rupture. So i have to run bulk 3x3x0.8 water and then add box to 3x3x9 to form interface. So if i want to run run bulk 3x3x0.8 water, how could i do? which FF should i use? the high T may be due to EM not success?? I believe you use the term bulk water in another sense as compared to all other guys here. When people say bulk liquid they imply the endless ocean of this liquid. It is not important what particular side lengths you have, since due to PBC you get infinitively large system. I suspect your teacher wants you to obtain a film of water that would be about 3 molecular layers wide. That's easy. Take your current box of water and apply editconf - editconf -f current_conf -o water_film_conf -box 3 3 3 Finally, just start MD run with a water_film_conf. You'll have the same periodic box , but water molecules will be present only at its center surrounded by vacuum in one (Z) direction. Happy GROMACSing, Dr. Vitaly V. Chaban Rochester, U.S.A. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re:Re: Re: water genbox 3x3x0.8 EM not successful T not high
On 12/17/10, gromacs ptf1...@163.com wrote: Yes. I should first run the 3x3x0.8 water to make the water in equilibrium. No. Any box dimension below about 2nm is nonsense with a normal force field. You want a film in vacuum, so use a box that is large enough to contain both the film and enough vacuum that the films cannot feel each other. So your box dimension in the direction normal to the film must be at least the thickness of the film plus twice rcoulomb. NVT will also be important for equilibration, per Vitaly's comments. You may also need to use a very short MD timestep - films are intrinsically less stable than bulk solvent, and the normal values are all for bulk, condensed media. Mark And then i use editconf to put the water at the centre of 3x3x9 box, so the film was 0.8 nm, the Z dimension is 9 nm, so there will be film. I want to simulate the rupture of the thickness of water film. If i directly put the 3x3x0.8 water in the 3x3x9 box, i will try to see the result. I At 2010-12-17 13:12:43，Vitaly Chaban vvcha...@gmail.com wrote: I still do not understand what physical system you want to create in the MD system or what phenomenon you want to reproduce. If you need a water film, then the only solution is to follow my former suggestion. In no case should you use 3x3x0.8 NPT MD box! If somebody suggested you to do such thing, then this person simply does not understand classical MD simulations. -- Dr.Vitaly V. Chaban On Thu, Dec 16, 2010 at 11:48 PM, gromacs ptf1...@163.com wrote: OK. I will use your method. But i am afraid there will be something wrong. Because generally, i should run the 3x3x0.8 NPT water, and then i use editconf to add the water to 3x3x3. If i donot run 3x3x0.8, i may not be able to run the final interface box. Because the water in the box is not at proper situation or position. Anyway, i will have a try first. If i have problem or success, i will give an answer to all. At 2010-12-17 09:51:57，Vitaly Chaban vvcha...@gmail.com wrote: Hey, gromacs - Nice to hear from you here... It is a bad idea to simulate something with any cartesian dimension lower than a couple of nanometers using classical FFs. All your problems are generated by 0.8 nm of the z-side. -- Dr. Vitaly V. Chaban Rochester, U.S.A. Thanks very much. I use the cutoff=0.38, because the cutoff should be smaller than the half box size. I guess it may be the Z dimension is too small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all results are OK. My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's rupture. So i have to run bulk 3x3x0.8 water and then add box to 3x3x9 to form interface. So if i want to run run bulk 3x3x0.8 water, how could i do? which FF should i use? the high T may be due to EM not success?? I believe you use the term bulk water in another sense as compared to all other guys here. When people say bulk liquid they imply the endless ocean of this liquid. It is not important what particular side lengths you have, since due to PBC you get infinitively large system. I suspect your teacher wants you to obtain a film of water that would be about 3 molecular layers wide. That's easy. Take your current box of water and apply editconf - editconf -f current_conf -o water_film_conf -box 3 3 3 Finally, just start MD run with a water_film_conf. You'll have the same periodic box , but water molecules will be present only at its center surrounded by vacuum in one (Z) direction. Happy GROMACSing, Dr. Vitaly V. Chaban Rochester, U.S.A. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Question about Extention simulation in REMD
Thanks! But still sth strange: I found the total energy is not identical between the last frame of the previous REMD and the first frame of the next REMD in one replica. last frame of the previous: 500.00 -372343.906250 first frame of the next: 0.00 -361778.375000 I wonder whether there's some problem and what caused it.. My setting In the .mdp of the previous simulation, gen_vel was on; I didn't record the velocity by putting nstvout =0; I used xtcgrp = Protein. Best Qin 2010/12/15 Justin A. Lemkul jalem...@vt.edu Qin Qiao wrote: Dear Sir or Madam, I wonder how to continue a REMD running using .cpt file in Gromacs 4.5.1. Since I ran a REMD of 56 replicas, there are one cpt file for each replica.. I couldn't do it by tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt I guess it's not for an iterative line in the answer in http://www.mail-archive.com/gmx-users@gromacs.org/msg33566.html, since the mdrun should run simultaneously. The iterative approach Mark describes in that post is for the tpbconv step. Simply extend all of your .tpr files to generate new ones (iterate over all your .tpr files), then proceed with mdrun as you would normally, making use of the -cpi feature. -Justin Could you give some advice? Thanks. Best, Qin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re:Re: Re: water genbox 3x3x0.8 EM not successful T not high
On 12/17/10, Mark Abraham mark.abra...@anu.edu.au wrote: On 12/17/10, gromacs ptf1...@163.com wrote: Yes. I should first run the 3x3x0.8 water to make the water in equilibrium. No. Any box dimension below about 2nm is nonsense with a normal force field. You want a film in vacuum, so use a box that is large enough to contain both the film and enough vacuum that the films cannot feel each other. So your box dimension in the direction normal to the film must be at least the thickness of the film plus twice rcoulomb. Or, use pbc=xy. See manual 7.3.9 Mark NVT will also be important for equilibration, per Vitaly's comments. You may also need to use a very short MD timestep - films are intrinsically less stable than bulk solvent, and the normal values are all for bulk, condensed media. Mark And then i use editconf to put the water at the centre of 3x3x9 box, so the film was 0.8 nm, the Z dimension is 9 nm, so there will be film. I want to simulate the rupture of the thickness of water film. If i directly put the 3x3x0.8 water in the 3x3x9 box, i will try to see the result. I At 2010-12-17 13:12:43，Vitaly Chaban vvcha...@gmail.com wrote: I still do not understand what physical system you want to create in the MD system or what phenomenon you want to reproduce. If you need a water film, then the only solution is to follow my former suggestion. In no case should you use 3x3x0.8 NPT MD box! If somebody suggested you to do such thing, then this person simply does not understand classical MD simulations. -- Dr.Vitaly V. Chaban On Thu, Dec 16, 2010 at 11:48 PM, gromacs ptf1...@163.com wrote: OK. I will use your method. But i am afraid there will be something wrong. Because generally, i should run the 3x3x0.8 NPT water, and then i use editconf to add the water to 3x3x3. If i donot run 3x3x0.8, i may not be able to run the final interface box. Because the water in the box is not at proper situation or position. Anyway, i will have a try first. If i have problem or success, i will give an answer to all. At 2010-12-17 09:51:57，Vitaly Chaban vvcha...@gmail.com wrote: Hey, gromacs - Nice to hear from you here... It is a bad idea to simulate something with any cartesian dimension lower than a couple of nanometers using classical FFs. All your problems are generated by 0.8 nm of the z-side. -- Dr. Vitaly V. Chaban Rochester, U.S.A. Thanks very much. I use the cutoff=0.38, because the cutoff should be smaller than the half box size. I guess it may be the Z dimension is too small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all results are OK. My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's rupture. So i have to run bulk 3x3x0.8 water and then add box to 3x3x9 to form interface. So if i want to run run bulk 3x3x0.8 water, how could i do? which FF should i use? the high T may be due to EM not success?? I believe you use the term bulk water in another sense as compared to all other guys here. When people say bulk liquid they imply the endless ocean of this liquid. It is not important what particular side lengths you have, since due to PBC you get infinitively large system. I suspect your teacher wants you to obtain a film of water that would be about 3 molecular layers wide. That's easy. Take your current box of water and apply editconf - editconf -f current_conf -o water_film_conf -box 3 3 3 Finally, just start MD run with a water_film_conf. You'll have the same periodic box , but water molecules will be present only at its center surrounded by vacuum in one (Z) direction. Happy GROMACSing, Dr. Vitaly V. Chaban Rochester, U.S.A. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Question about Extention simulation in REMD
On 12/17/10, Qin Qiao qiaoqi...@gmail.com wrote: Thanks! But still sth strange: I found the total energy is not identical between the last frame of the previous REMD and the first frame of the next REMD in one replica. last frame of the previous: 500.00 -372343.906250 first frame of the next: 0.00 -361778.375000 I wonder whether there's some problem and what caused it.. OK, we'll need to see the exact sequence of commands that produced your observations, i.e. mdrun, then tpbconv, then mdrun. The fact that you're managing to get the time reset to zero indicates you've done something wrong. As a guess, you didn't use the right .cpt file with the second mdrun -cpi. My setting In the .mdp of the previous simulation, gen_vel was on; I didn't record the velocity by putting nstvout =0; I used xtcgrp = Protein. These don't matter. Mark Best Qin 2010/12/15 Justin A. Lemkul jalem...@vt.edu Qin Qiao wrote: Dear Sir or Madam, I wonder how to continue a REMD running using .cpt file in Gromacs 4.5.1. Since I ran a REMD of 56 replicas, there are one cpt file for each replica.. I couldn't do it by tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt I guess it's not for an iterative line in the answer in http://www.mail-archive.com/gmx-users@gromacs.org/msg33566.html, since the mdrun should run simultaneously. The iterative approach Mark describes in that post is for the tpbconv step. Simply extend all of your .tpr files to generate new ones (iterate over all your .tpr files), then proceed with mdrun as you would normally, making use of the -cpi feature. -Justin Could you give some advice? Thanks. Best, Qin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu(http://vt.edu) | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
