Hi Mark,
I have used the following .mdp file for the run and got the excess
temperature for the system; it has reached the desired temp at around
150-155 ps. But I need to reach the temp at after 300 ps.
Thanks,
define = -DFLEXIBLE
constraints= h-bonds
integrator
Dear All,
the Gromacs User Manual V.4.5.4 states on p. 33: (...) the surface
tension and the z-component of the pressure can be coupled to a pressure
bath. Presently, this only works with the Berendsen pressure coupling
algorithm in GROMACS.
My question: does this hold for V. 4.5.5 as well?
Dear Justin,
Thank you very much for your answer.
I specified each molecule individually in index file and I used trjconv -sep
command
to seperate the system each step (conf1.gro, conf2.gro, conf3.gro,
conf4.gro). Then
I used script that you suggested, it was as;
groups=`grep ^\[ index.ndx |
Dear gmx users,
How can I calculate the time evolutions of an angle in the molecules in the
system?
Thanks,
Akn.
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On 13/08/2012 10:03 PM, akn wrote:
Dear Justin,
Thank you very much for your answer.
I specified each molecule individually in index file and I used trjconv -sep
command
to seperate the system each step (conf1.gro, conf2.gro, conf3.gro,
conf4.gro). Then
I used script that you suggested, it was
On 13/08/2012 10:11 PM, akn wrote:
Dear gmx users,
How can I calculate the time evolutions of an angle in the molecules in the
system?
Various ways. Check out manual section 7.4 for clues, and chapter 8 and
appendix D for more details.
Mark
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I have written a unique MD program and want to output a full-precision
trajectory containing coordinate, velocity, and force information in a .trr
or a .trj formatted file.
Where in the gromacs code can I find a description of the formats of these
files and an example of how they are written?
Hi,
I have read a couple of posts on related topics but I am still not
sure how to proceed and would be grateful to get some help.
I want to run implicit solvent simulations of a protein+water
(implicit) system in the canonical ensemble using charmm27+cmap
forcefield. I am trying to use the
As these are binary files the formatting can be quite complex I would
suggest using the library available here:
http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
This includes all the functions necessary to read/write these formats and is
licensed under LGPL.
Richard
On
Dear gmx users,
I'm simulating a system of protein and water. In NPT equilibration step, I get
the error of too many warnings.
Anybody knows about this warning?
The warning is :
WARNING 1 [file NPT.mdp]:
You are using pressure coupling with absolute position restraints, this
will give
Dear All
I want to do simulation of some ions like azide ion,thiocynate ion and
other inorganic compounds in liquid water.
I am not sure how to generate topology file for the same.How can I go
about doing the same.
--
DeepaK Ojha
School Of Chemistry
Selfishness is not living as one wishes to
Dear gmx users,
I'm simulating a system of protein and water. In NPT equilibration step, I get
the error of too many warnings.
Anybody knows about this warning?
The warning is :
WARNING 1 [file NPT.mdp]:
You are using pressure coupling with absolute position restraints, this
will give
Hello all,
I am going to restart my crashed simulations, but I am not sure which
of *_prev.cpt or *.cpt to use as they contain different written
frames.
*_prev.cpt Last frame -1 time 7462.900
*.cptLast frame -1 time 7468.965
Also on the gmx site it is stated
Long story short: backup everything (since it's a backup, and hopefully
you won't need it), then use the [whatever].cpt file. You don't want to
do work twice, do you? If you use the [whatever]_prev.cpi file, you will
calculate some frames *again* that are already there.
If you use an up-to-date
On 8/13/12 12:36 PM, Shima Arasteh wrote:
Dear gmx users,
I'm simulating a system of protein and water. In NPT equilibration step, I get
the error of too many warnings.
Anybody knows about this warning?
Yes, and there are several posts in the list archive explaining its origin,
On 8/13/12 1:49 PM, Deepak Ojha wrote:
Dear All
I want to do simulation of some ions like azide ion,thiocynate ion and
other inorganic compounds in liquid water.
I am not sure how to generate topology file for the same.How can I go
about doing the same.
Likely you will have to do it
Thank you. I am using
mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x -cpi md_prev.cpt
but I dont get any output and the issued command terminates in the terminal.
Do I have to remove the -o -c -g -e -x flags from the command line?
Appreciate your help,
On 13 August 2012 15:28,
On 8/13/12 3:42 PM, Juliette N. wrote:
Thank you. I am using
mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x -cpi md_prev.cpt
but I dont get any output and the issued command terminates in the terminal.
Normally error messages are rather obvious. Check your .log file carefully or
OK, thanks.
But please let me know something:
Is the pressure coupling with absolute position restraints is an option to
fix a volume significantly? If yes, then It's me to think about keeping fix
the volume of my system or not.
Thanks, believe me I got this point through the mailing list :-)
On 2012-08-13 21:39, Justin Lemkul wrote:
On 8/13/12 1:49 PM, Deepak Ojha wrote:
Dear All
I want to do simulation of some ions like azide ion,thiocynate ion and
other inorganic compounds in liquid water.
I am not sure how to generate topology file for the same.How can I go
about doing the
Am 13.08.2012 21:42, schrieb Juliette N.:
Thank you. I am using
mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x -cpi md_prev.cpt
I see a md_prev.cpt. If I presume correctly that this is for the
continuation of the crashed run: Why and did you read what I wrote?
but I dont get any
On 8/13/12 3:47 PM, Shima Arasteh wrote:
OK, thanks.
But please let me know something:
Is the pressure coupling with absolute position restraints is an option to
fix a volume significantly? If yes, then It's me to think about keeping fix the volume
of my system or not.
You can't have
Yes this is to continue a crashed run, but I dont know why my runs
crash at the very beginnig of the simulation. I am using 4.5.4 so
-append should work by default. I tried a simulation from time zero
and it works as before ( mpirun -np 8 mdrun_mpi -deffnm md -s -o -c
-g -e -x ) but as soon as I
On 8/13/12 4:08 PM, Juliette N. wrote:
Yes this is to continue a crashed run, but I dont know why my runs
crash at the very beginnig of the simulation. I am using 4.5.4 so
-append should work by default. I tried a simulation from time zero
and it works as before ( mpirun -np 8 mdrun_mpi
Sorry Justin, but I dont see whats happening...
Do I have to remove mpi or -np from the line while using -cpi *.cpt ?
mdrun -deffnm md -s -o -c -g -e -x -cpi output
Thanks!
On 13 August 2012 16:10, Justin Lemkul jalem...@vt.edu wrote:
On 8/13/12 4:08 PM, Juliette N. wrote:
Yes this is
On 8/13/12 4:16 PM, Juliette N. wrote:
Sorry Justin, but I dont see whats happening...
Do I have to remove mpi or -np from the line while using -cpi *.cpt ?
No, you don't. All you should need (provided the .cpt file is valid, which it
appears to be from the gmxcheck output from before)
I am using the same line, but it crashes...Is that because my trr
files is big that it cand append the files? It was ~ 40 GB when crash
happened...
I am using 4.5.4. I tried both with and without -append.
On 13 August 2012 16:19, Justin Lemkul jalem...@vt.edu wrote:
On 8/13/12 4:16 PM,
On 8/13/12 4:34 PM, Juliette N. wrote:
I am using the same line, but it crashes...Is that because my trr
files is big that it cand append the files? It was ~ 40 GB when crash
happened...
I am using 4.5.4. I tried both with and without -append.
If it fails with and without the -append
Thanks, maybe I should re start ... :(
On 13 August 2012 16:36, Justin Lemkul jalem...@vt.edu wrote:
On 8/13/12 4:34 PM, Juliette N. wrote:
I am using the same line, but it crashes...Is that because my trr
files is big that it cand append the files? It was ~ 40 GB when crash
happened...
Hi all,
My cpt file doesnt contain any information?!!
gmxcheck -f md.cpt gives the following:
Checking file md.cpt
# Atoms 20688
Last frame -1 time 7468.965
Item#frames Timestep (ps)
Step 1
Time 1
Lambda 1
Coords 1
On 8/13/12 4:54 PM, Juliette N. wrote:
Hi all,
My cpt file doesnt contain any information?!!
Sure it does.
gmxcheck -f md.cpt gives the following:
Checking file md.cpt
# Atoms 20688
Last frame -1 time 7468.965
Item#frames Timestep (ps)
Step 1
All right, but I was expecting some more information reflecting the
last state of the system, e.g, velocities...
Thank you,
On 13 August 2012 17:04, Justin Lemkul jalem...@vt.edu wrote:
On 8/13/12 4:54 PM, Juliette N. wrote:
Hi all,
My cpt file doesnt contain any information?!!
Sure
Oh something I didn't mention: for bond constraints I used h-bonds instead
of all-bonds. This may or may not make a difference (although I switched to
h-bonds based on the suggestion of some charmm/lipid thread on here from
a couple of years ago).
On 2012-08-09 12:34:19PM -0300, Sebastien Cote
Dear Gromacs Users,
I have some questions regarding GB-Polarization Energy Calculation
with Gromacs. I will be grateful if someone can help me with the
answers.
I am trying to calculate GB-Polarization energy for different Protein
molecules. I am interested both in energy values with the time
From your comments, it appears that you have not watched the trajectory for
you system. This is really something that everyone should do with the systems
they are simulating, as you can gain a lot of information from looking
visually at it. Looking at 0.5ns snap shots is not watching the
On 8/13/12 5:10 PM, Juliette N. wrote:
All right, but I was expecting some more information reflecting the
last state of the system, e.g, velocities...
gmxcheck verifies the integrity of the file. gmxdump will produce more detailed
information, not that it's of any particular use in this
Greetings all,
Can I easily obtain the potential energy for a energy group rather than the
whole simulation cell? Does it make any sense to do so?
I am simulating protein ligand complexes and have observed movement in some
cases. When I analyse the interaction energy sum of LJ and columbic of
Hello everyone,
I have a doubt about LIE calculation using g_lie in gromacs. This doubt is
about the values automatically assigned for -Clj and -Cqq flags when I ran
the following command:
$ g_lie -f J32_md10ns.edr -o LIE_1A1_J32.xvg -b 7001 -e 1 -ligand J32
The following text contains my
Dear All,
Is there any way to add a specific number of water ( let say 650
water) molecules while dissolving the solute in a given box ?
Thanks,
Tarak
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On 14/08/2012 7:53 AM, Dallas Warren wrote:
From your comments, it appears that you have not watched the trajectory for
you system. This is really something that everyone should do with the systems
they are simulating, as you can gain a lot of information from looking visually at
it.
On 14/08/2012 6:08 AM, Juliette N. wrote:
Yes this is to continue a crashed run, but I dont know why my runs
crash at the very beginnig of the simulation.
You have to look at the stderr, stdout and .log file for information.
You can't solve the problem without that.
Mark
I am using
On 14/08/2012 11:07 AM, Tom Dupree wrote:
Greetings all,
Can I easily obtain the potential energy for a energy group rather than the
whole simulation cell?
Yes. See manual 3.3 and 7.3.8. But below you imply you're already doing
this. You can make custom groups - see
On 14/08/2012 2:23 AM, Broadbent, Richard wrote:
As these are binary files the formatting can be quite complex I would
suggest using the library available here:
http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
This includes all the functions necessary to read/write these
Thanks for the quick reply, I have given this command to add 612 water
molecules.
genbox -cs spc216 -nmol 612 -cp ala_box.gro -o ala_solv.gro -p ala.top
But in the solvated file, I see there are 668 water molecules.
A part of the output while adding water molecules is as follows
Using plugin
Did you have waters in the system before adding another 612?
I don't know how VMD counts waters, but another way is to grep -c for SOL in
the resulting gro file and divide by 3.
On 2012-08-14 10:07:54AM +0530, tarak karmakar wrote:
Thanks for the quick reply, I have given this command to add
On 14/08/2012 1:07 AM, Sai Pooja wrote:
Hi,
I have read a couple of posts on related topics but I am still not
sure how to proceed and would be grateful to get some help.
I want to run implicit solvent simulations of a protein+water
(implicit) system in the canonical ensemble using
This is the ala.gro (alanine dipeptide) file which does not contain
any water (SOL) a priori.
Grunge ROck MAChoS
22
1ACE HH311 1.267 1.058 1.673
1ACECH32 1.364 1.086 1.631
1ACE HH323 1.422 0.996 1.607
1ACE HH334 1.416 1.148
On 14/08/2012 2:37 PM, tarak karmakar wrote:
Thanks for the quick reply, I have given this command to add 612 water
molecules.
genbox -cs spc216 -nmol 612 -cp ala_box.gro -o ala_solv.gro -p ala.top
That's not how to use -nmol, nor is it the right option to solve your
problem. There's an
hmm. What happens if you try -maxsol instead of -nmol?
On 2012-08-14 10:24:18AM +0530, tarak karmakar wrote:
This is the ala.gro (alanine dipeptide) file which does not contain
any water (SOL) a priori.
Grunge ROck MAChoS
22
1ACE HH311 1.267 1.058 1.673
1ACE
You need to assign your own experimentally determined values to -Elj and -Eqq.
These are determined by simulating your ligand in a solvent box.
g_lie uses some common values found in the literature for -Clj and -Cqq again
you need to decide if they are appropriate in your case. Try reading papers
On 14/08/2012 7:38 AM, jesmin jahan wrote:
Dear Gromacs Users,
I have some questions regarding GB-Polarization Energy Calculation
with Gromacs. I will be grateful if someone can help me with the
answers.
I am trying to calculate GB-Polarization energy for different Protein
molecules. I am
On 13/08/2012 7:21 PM, Felipe Pineda, PhD wrote:
Dear All,
the Gromacs User Manual V.4.5.4 states on p. 33: (...) the surface
tension and the z-component of the pressure can be coupled to a
pressure bath. Presently, this only works with the Berendsen pressure
coupling algorithm in GROMACS.
Dear Tom,
The explanation really helps me understand LIE much more clearer.
What's the issue if I have used PME coulombtype? I have actually used PME.
Thanks,
Peterson J
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Sent
Oh !!
I got it it is not the -nmol but '-maxmol'
thanks to both of u...:)
On Tue, Aug 14, 2012 at 10:35 AM, Peter C. Lai p...@uab.edu wrote:
hmm. What happens if you try -maxsol instead of -nmol?
On 2012-08-14 10:24:18AM +0530, tarak karmakar wrote:
This is the ala.gro (alanine
sorry '-maxsol'
On Tue, Aug 14, 2012 at 11:24 AM, tarak karmakar tarak20...@gmail.com wrote:
Oh !!
I got it it is not the -nmol but '-maxmol'
thanks to both of u...:)
On Tue, Aug 14, 2012 at 10:35 AM, Peter C. Lai p...@uab.edu wrote:
hmm. What happens if you try -maxsol instead of
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