On Wed, Nov 6, 2013 at 8:22 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/6/13 2:14 PM, Ehsan Sadeghi wrote:
Many thanks Justin. What is an appropriate cut-off value? My box size is
d=
0.5 nm; based on the definition of cut-off radius, its value shouble be
smaller than d/2; therefore
On 11/6/13 4:52 PM, Mark Abraham wrote:
On Wed, Nov 6, 2013 at 8:22 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/6/13 2:14 PM, Ehsan Sadeghi wrote:
Many thanks Justin. What is an appropriate cut-off value? My box size is
d=
0.5 nm; based on the definition of cut-off radius, its value
Dear Justin,
I am sorry for the late reply. I still can't figure it out.
Could you please send me the mdp file which was used for your single point
calculations.
I want to do some comparison and then solve the problem.
Thanks very much!
All the best,
Qinghua
--
View this message in context:
I've gone to conclusion that simulation with 1 or 2 GPU simultaneously gave
me the same performance
mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v -deffnm md_CaM_test,
mdrun -ntmpi 2 -ntomp 6 -gpu_id 0 -v -deffnm md_CaM_test,
Doest it be due to the small CPU cores or addition RAM ( this system has 32
Does it make more sense to use nose-hoover or v-rescale when running in
implicit solvent GBSA? I understand that this might be a matter of
opinion.
Thanks,
Gianluca
-
Gianluca Interlandi, PhD gianl...@u.washington.edu
Hi Debashis,
Makes sure that the anion and receptor are together in the reference
structure you use for trjconv -pbc nojump
Cheers,
Tsjerk
On Tue, Nov 5, 2013 at 8:12 AM, Debashis Sahu debashis.sah...@gmail.comwrote:
Dear All,
I have an problem related to jumping trajectory.
Hi,
I am getting the following error while using the command -
[root@localhost INGT]# mpirun -np 24 mdrun_mpi -v -deffnm npt
Error -
/usr/bin/mpdroot: open failed for root's mpd conf
filempiexec_localhost.localdomain (__init__ 1208): forked process failed;
status=255
I complied gromacs using
Dear GMX Users
I am using parmbsc0 force field to study DNA-ligand interaction but my problem
is free energy calculation (MMPBSA) for this interaction. How can I calculate
free energy using MMPBSA approach?
Thank you very much for your time and consideration.
Best Regards
Kiana
--
Dear all,
I'm going to perform a molecular dynamics simulation on a protein. As a
default the simulation gives one final *.gro file. I need to get a .gro
file after each say 500 ps of my simulation, in addition of the final file.
How can I do so?
Best regards,
Sarah Keshavarz
--
gmx-users
Dear Sarah,
you have to use the trjconv command with the flags -b -e and -sep.
For example: trjconv -f xxx.trr -s xxx.tpr -o out.gro -b (initial frame
to read in ps) -e (last frame to read in ps) -sep
Regards
El mar, 05-11-2013 a las 01:04 -0800, sarah k escribió:
Dear all,
I'm going to
Just out of curiosity -why can you only choose between GROMOS force fields?
2013/11/5 pratibha kapoor kapoorpratib...@gmail.com
Dear all
I would like to carry out unfolding simulations of my dimeric protein and
would like to know which is the better force field to work with out of
gromos
My suggestions:
1) During compilstion using -march=corei7-avx-i I have obtained error that
somethng now found ( sorry I didnt save log) so I compile gromacs without
this flag
2) I have twice as better performance using just 1 gpu by means of
mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v -deffnm
Hi,
Whenever I am trying to do position retrained MD run, It has been stopped
at middle of the MD run. I have given the following error. Can you please
suggest me something to resolve this error?
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax
Dear James,
On 05/11/13 11:16, James Starlight wrote:
My suggestions:
1) During compilstion using -march=corei7-avx-i I have obtained error that
somethng now found ( sorry I didnt save log) so I compile gromacs without
this flag
2) I have twice as better performance using just 1 gpu by means
On 05.11.2013 10:04, sarah k wrote:
I'm going to perform a molecular dynamics simulation on a protein. As a
default the simulation gives one final *.gro file. I need to get a .gro
file after each say 500 ps of my simulation, in addition of the final file.
How can I do so?
Riccardo already gave
Dear Richard,
1) mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v -deffnm md_CaM_test
gave me performance about 25ns/day for the explicit solved system consisted
of 68k atoms (charmm ff. 1.0 cutoofs)
gaves slightly worse performation in comparison to the 1)
finally
3) mdrun -deffnm md_CaM_test
running
What does your curve look like? What parameters are you using in the mdp?
How big is your system and what kind of molecules are in there? Providing
this kind of information would help people work out what the problem is.
Then again it may be ok that the minimisation has converged without
reaching
On 11/5/13 6:28 AM, Kalyanashis Jana wrote:
Hi,
Whenever I am trying to do position retrained MD run, It has been stopped
at middle of the MD run. I have given the following error. Can you please
suggest me something to resolve this error?
Energy minimization has stopped, but the forces
On 11/5/13 3:45 AM, kiana moghaddam wrote:
Dear GMX Users
I am using parmbsc0 force field to study DNA-ligand interaction but my problem
is free energy calculation (MMPBSA) for this interaction. How can I calculate
free energy using MMPBSA approach?
Thank you very much for your time and
I have given my .mdp file,
; title = trp_drg
warning = 10
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 100 ; total 2000.0 ps.
Dear Justin,
Can you please tell me, how I can solve this problem?? If I will change
the coordinate of atom 15461, will it help me? But you know, I did this
step changing the position of drug molecule and I got same error.
On Tue, Nov 5, 2013 at 5:44 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/5/13 7:19 AM, Kalyanashis wrote:
I have given my .mdp file,
; title = trp_drg
warning = 10
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps
On 11/5/13 7:31 AM, Kalyanashis Jana wrote:
Dear Justin,
Can you please tell me, how I can solve this problem?? If I will change
the coordinate of atom 15461, will it help me? But you know, I did this
step changing the position of drug molecule and I got same error.
You should first do
Dear Users,
I am running MD simulations of a protein-ligand system. Sometimes when i do
an mdrun, be it for the energy minimization or during the nvt and npt
equillibration or the actual md run step, sometimes the output files are
named in a very odd way (strange extensions) e.g em.gro.tprr or
On 11/5/13 7:37 AM, MUSYOKA THOMMAS wrote:
Dear Users,
I am running MD simulations of a protein-ligand system. Sometimes when i do
an mdrun, be it for the energy minimization or during the nvt and npt
equillibration or the actual md run step, sometimes the output files are
named in a very odd
Dear Kiana,
You can contact with Paissoni Cristina (email: paissoni.crist...@hsr.it) to
get tool using MM/PBSA with GROMACS.
Hope it help :)
Cheers,
Kieu Thu
On Tue, Nov 5, 2013 at 7:18 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/5/13 3:45 AM, kiana moghaddam wrote:
Dear GMX Users
Dear Dr Justin,
Much appreciation. You nailed it.
Kind regards.
On Tue, Nov 5, 2013 at 2:41 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/5/13 7:37 AM, MUSYOKA THOMMAS wrote:
Dear Users,
I am running MD simulations of a protein-ligand system. Sometimes when i
do
an mdrun, be it for the
Dear All,
I intend to run a membrane-protein system in GPU. I am slightly confused
about the .mdp settings
Non-gpu settings (according to original CHARMM FF paper):
rlist = 1.0
rlistlong= 1.4
rvdw_switch = 0.8
vdwtype= Switch
On Tue, Nov 5, 2013 at 12:55 PM, James Starlight jmsstarli...@gmail.comwrote:
Dear Richard,
1) mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v -deffnm md_CaM_test
gave me performance about 25ns/day for the explicit solved system consisted
of 68k atoms (charmm ff. 1.0 cutoofs)
gaves slightly worse
Hi,
I need to replace an atom with another in the considered system.
I'd like to know if it is possible and if so what changes I need to do.
thanks
j.rahrow
On Thu, Oct 31, 2013 at 12:47 PM, J Alizadeh j.alizade...@gmail.com wrote:
Hi,
I need to replace an atom with another in the
29420 Atoms with a some tuning of the write out and communication intervals:
nodes again: 2 x Xeon E5-2680v2 + 2 x NVIDIA K20X GPGPUs @ 4fs vsites
1 node 212 ns/day
2 nodes 295 ns/day
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*
Dear Riccardo Concu and Mirco Wahab,
Thanks for your perfect responses.
Regards,
Sarah
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
*
On 11/5/13 10:34 AM, J Alizadeh wrote:
Hi,
I need to replace an atom with another in the considered system.
I'd like to know if it is possible and if so what changes I need to do.
The coordinate file replacement is trivial. Just open the file in a text editor
and repname the atom. The
I wonder whether increasing the surface tension parameter
sa-surface-tension might solve the problem with the protein unfolding.
Thanks,
Gianluca
On Mon, 4 Nov 2013, Gianluca Interlandi wrote:
Hi Justin,
We are using infinite cutoffs (all vs all). Here is the mdp file for the
heating
You need to configure your MPI environment to do so (so read its docs).
GROMACS can only do whatever that makes available.
Mark
On Tue, Nov 5, 2013 at 2:16 AM, bharat gupta bharat.85.m...@gmail.comwrote:
Hi,
I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having
32
Timo,
Have you used the default settings, that is one rank/GPU? If that is
the case, you may want to try using multiple ranks per GPU, this can
often help when you have 4-6 cores/GPU. Separate PME ranks are not
switched on by default with GPUs, have you tried using any?
Cheers,
--
Szilárd Páll
Hi Mike,
I have similar configurations except a cluster of AMD-based linux
platforms with 2 GPU cards.
Your suggestion works. However, the performance of 2 GPU discourages
me because , for example, with 1 GPU, our computer node can easily
obtain a simulation of 31ns/day for a protein
Hi Timo,
Can you provide a benchmark with 1 Xeon E5-2680 with 1 Nvidia
k20x GPGPU on the same test of 29420 atoms ?
Are these two GPU cards (within the same node) connected by a SLI (Scalable
Link Interface) ?
Thanks,
Dwey
--
View this message in context:
Hi Dwey,
First and foremost, make sure to read the
http://www.gromacs.org/Documentation/Acceleration_and_parallelization
page, in particular the Multiple MPI ranks per GPU section which
applies in your case.
Secondly, please do post log files (pastebin is your friend), the
performance table at
On Tue, Nov 5, 2013 at 9:55 PM, Dwey Kauffman mpi...@gmail.com wrote:
Hi Timo,
Can you provide a benchmark with 1 Xeon E5-2680 with 1 Nvidia
k20x GPGPU on the same test of 29420 atoms ?
Are these two GPU cards (within the same node) connected by a SLI (Scalable
Link Interface) ?
Hi Szilard,
Thanks for your suggestions. I am indeed aware of this page. In a 8-core
AMD with 1GPU, I am very happy about its performance. See below. My
intention is to obtain a even better one because we have multiple nodes.
### 8 core AMD with 1 GPU,
Force evaluation time GPU/CPU: 4.006
Hi Szilard,
Thanks.
From Timo's benchmark,
1 node142 ns/day
2 nodes FDR14 218 ns/day
4 nodes FDR14 257 ns/day
8 nodes FDR14 326 ns/day
It looks like a infiniband network is required in order to scale up when
running a task across nodes. Is it correct ?
Dwey
--
View
Thank you for the pointer Michael.
couple-intramol = no
What a diff of the output from gmxdump of the two tpr files shows is in both of
these cases (normal and double charged), when:
lambda is set to 1.0 (atoms within both molecules will have zero charge)
lambda is set to 0.00
Thanks for the suggestion Chris. Had a quick look and can't see easily how to
do this, but I think I am at a point now where it is not an issue and don't
have to actually do this.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences,
Message: 5
Date: Mon, 04 Nov 2013 13:32:52 -0500
From: Justin Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Analysis tools and triclinic boxes
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 5277e854.9000...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1;
Hi Szilárd and all,
Thanks very much for the information. I am more interested in getting
single simulations to go as fast as possible (within reason!) rather than
overall throughput. Would you expect that the more expensive dual
Xeon/Titan systems would perform better in this respect?
Cheers
Yes, that has been true for GROMACS for a few years. Low-latency
communication is essential if you want a whole MD step to happen in around
1ms wall time.
Mark
On Nov 5, 2013 11:24 PM, Dwey Kauffman mpi...@gmail.com wrote:
Hi Szilard,
Thanks.
From Timo's benchmark,
1 node142
Your best bet is probably to center everything on the receptor. That will
prevent jumping of the receptor only, which is hopefully all you need.
-Trayder
On Tue, Nov 5, 2013 at 7:14 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Debashis,
Makes sure that the anion and receptor are
Dear users,
When the simulation was carried out with PME
rcoulomb was set equal to rlist. But when I need to
to ligand-water simulation without PME (with RF-0)
then it requires rlist greater by 0.1-0.3 than rcoulomb.
So if I rerun protein-ligand-water simulation there
could be more differences in
Hi,
I want to know the exact way to calculate the density of water around
certain residues in my protein. I tried to calculate this by using
g_select, with the following command :-
g_select -f nvt.trr -s nvt.tpr -select Nearby water resname SOL and
within 0.5 of resnr 115 to 118 -os water.xvg
Hello Dear GROMACS users,
I trying to do a MD calculation using GROMACS, but when I running pdb2gmx I
get the following error:
Fatal error:
Residue '' not found in residue topology database
I'm a beginner GROMACS user, but I want to know exactly, how add my
residues to GROMACS step by step?.
Dear Justin
Further to your previous email, I want to calculate free energy for DNA-ligand
interaction. According to your answer, for more sensitive calculations like
free energy simulations and normal modes, emtol should be lower than 1. As I
understand, you mean that for these systems emtol
Hello Archana,
I'm also toying with a TFE-water system, therefore I am also a newbie. This
is what I am doing, I hope it helps:
1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I
don't use PRODGR, see why in DOI: 10.1021/ci100335w).
2) Do the math and check how many
That should be enough. You may want to use the -march (or equivalent)
compiler flag for CPU optimization.
Cheers,
--
Szilárd Páll
On Sun, Nov 3, 2013 at 10:01 AM, James Starlight jmsstarli...@gmail.com wrote:
Dear Gromacs Users!
I'd like to compile lattest 4.6 Gromacs with native GPU
Hi,
I was wondering if anyone could help me with the gmxcheck function? In the
manual it is written, -m flag is given a LaTeX file will be written
consisting of a rough outline for a methods section for a paper.
I tried it several times but there isn't any file that I can see.
I had run some
Erratum:
Where I wrote I ended up going with the former it should be I ended up
going with the latter.
/J
On Mon, Nov 4, 2013 at 10:47 AM, João Henriques
joao.henriques.32...@gmail.com wrote:
Hello Archana,
I'm also toying with a TFE-water system, therefore I am also a newbie.
This is
Hi,
I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works
fine till .configure command, but I am getting error at the make command :-
Error:
[root@cluster gromacs-4.5.7]# make
/bin/sh ./config.status --recheck
running CONFIG_SHELL=/bin/sh /bin/sh
Hello,
I would like to
simulate a membrane system with two walls, one at the bottom of my box
at z=0 and one at the top, using the gromos53a6 forcefield (GROMACS
version 4.5.5).
My testing system consists of a membrane in the
middle, water and sodium ions (40xNa+) above the membrane and water
Hi,
I want to know the exact way to calculate the density of water around
certain residues in my protein. I tried to calculate this by using
g_select, with the following command :-
g_select -f nvt.trr -s nvt.tpr -select Nearby water resname SOL and
within 0.5 of resnr 115 to 118 -os water.xvg
Hi,
I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works
fine till .configure command, but I am getting error at the make command :-
Error:
[root@cluster gromacs-4.5.7]# make
/bin/sh ./config.status --recheck
running CONFIG_SHELL=/bin/sh /bin/sh
Szilárd, thanks for suggestion!
What kind of CPU optimisation should I take into account assumint that I'm
using dual-GPU Nvidia TITAN workstation with 6 cores i7 (recognized as 12
nodes in Debian).
James
2013/11/4 Szilárd Páll pall.szil...@gmail.com
That should be enough. You may want to
On 11/4/13 1:31 AM, Gianluca Interlandi wrote:
Is there a way to tell from the log file whether positional restraints are
really activated or not?
Yes, there is a position restraint energy term written to the .log and .edr
files if the restraints are active.
-Justin
--
On 11/4/13 1:52 AM, Saman Shahriyari wrote:
dear gmx users
i am trying to use g_lie tool regarding the fact i am a
newbie to this. so i searched through the web for an appropriate
protocol. although there are lots of staffs discussing the theory, but i
couldn't find any thing describing
On 11/4/13 3:16 AM, Ramon Valencia wrote:
Hello Dear GROMACS users,
I trying to do a MD calculation using GROMACS, but when I running pdb2gmx I
get the following error:
Fatal error:
Residue '' not found in residue topology database
I'm a beginner GROMACS user, but I want to know exactly,
On 11/4/13 3:29 AM, kiana moghaddam wrote:
Dear Justin
Further to your previous email, I want to calculate free energy for DNA-ligand
interaction. According to your answer, for more sensitive calculations like
free energy simulations and normal modes, emtol should be lower than 1. As I
On 11/4/13 5:06 AM, Ankita Naithani wrote:
Hi,
I was wondering if anyone could help me with the gmxcheck function? In the
manual it is written, -m flag is given a LaTeX file will be written
consisting of a rough outline for a methods section for a paper.
I tried it several times but there
Hi Justin,
Thank you for your reply. I did give the .tpr file but the job terminated
after few frames only. Also, if that is not helpful, do you have any
suggestions to recover the essential information which you would include as
part of methods?
Kind regards,
Ankita
On Mon, Nov 4, 2013 at
On 11/4/13 7:14 AM, Ankita Naithani wrote:
Hi Justin,
Thank you for your reply. I did give the .tpr file but the job terminated
after few frames only. Also, if that is not helpful, do you have any
There are no frames in a .tpr file. I suspect you're simply issuing the command
incorrectly,
I do have the .mdp file. Main thing I was concerned about were details like
number of water molecules added and number of counter ions added. Does
gmxdump output that information?
On Mon, Nov 4, 2013 at 12:19 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/4/13 7:14 AM, Ankita Naithani
On 11/4/13 7:37 AM, Ankita Naithani wrote:
I do have the .mdp file. Main thing I was concerned about were details like
number of water molecules added and number of counter ions added. Does
gmxdump output that information?
Yes, buried in a long list of other things. Trivial details like
just a small benchmark...
each node - 2 x Xeon E5-2680v2 + 2 x NVIDIA K20X GPGPUs
42827 atoms - vsites - 4fs
1 node142 ns/day 2 nodes FDR14 218 ns/day
4 nodes FDR14 257 ns/day
8 nodes FDR14 326 ns/day
16 nodes FDR14 391 ns/day (global warming)
best,
timo
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gmx-users mailing list
Thanks Justin very much for your help. (Extremely silly and unthoughtful of
me to forget this)
Kind regards,
Ankita
On Mon, Nov 4, 2013 at 12:40 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/4/13 7:37 AM, Ankita Naithani wrote:
I do have the .mdp file. Main thing I was concerned about
Dear Justin
It is obvious that emtol value can not be zero or negative. but you wrote in
your email For more sensitive calculations like free energy simulations and
normal modes, you will want to minimize much more thoroughly (for NM, emtol
1) and in double precision. what did you mean by
On 11/4/13 8:55 AM, kiana moghaddam wrote:
Dear Justin
It is obvious that emtol value can not be zero or negative. but you wrote in
your email For more sensitive calculations like free energy simulations and
normal modes, you will want to minimize much more thoroughly (for NM, emtol
1) and
Brad,
These numbers seems rather low for a standard simulation setup! Did
you use a particularly long cut-off or short time-step?
Cheers,
--
Szilárd Páll
On Fri, Nov 1, 2013 at 6:30 PM, Brad Van Oosten bv0...@brocku.ca wrote:
Im not sure on the prices of these systems any more, they are
Hi David,
Do you want to maximize throughput with multiple simulations or you
want single simulations as fast as possible?
In general, as few and fast CPU(s)/GPU(s) is best - especially with
such small systems as yours which won't scale very well to more than
1-2 GPUs. As I previously mentioned
You can use the -march=native flag with gcc to optimize for the CPU
your are building on or e.g. -march=corei7-avx-i for Intel Ivy Bridge
CPUs.
--
Szilárd Páll
On Mon, Nov 4, 2013 at 12:37 PM, James Starlight jmsstarli...@gmail.com wrote:
Szilárd, thanks for suggestion!
What kind of CPU
On Mon, Nov 4, 2013 at 12:01 PM, bharat gupta bharat.85.m...@gmail.comwrote:
Hi,
I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works
fine till .configure command, but I am getting error at the make command :-
Error:
[root@cluster gromacs-4.5.7]#
Hello
I am just trying to do a simple MD on a dimmer system (in which the dimmers are
NOT identical). I can use pdb2gmx to create a topology file and four .itp
files pores.chainA.itp, pores.chainX.itp; system.Protein.chainA.itp and
system.Protein.chainX.itp.
When I use grompp however, I
Dear all,
I am using gromacs 4.6.3 with a triclinic box. Based on the manual and mail
list, it is my understanding that the default box shape in gromacs in a
triclinic box. Can I assume that all the analysis tools also work for a
triclinic box.
Cheers,
Stephanie
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On 11/4/13 1:29 PM, Steve Seibold wrote:
Hello
I am just trying to do a simple MD on a dimmer system (in which the dimmers are
NOT identical). I can use pdb2gmx to create a topology file and four .itp
files pores.chainA.itp, pores.chainX.itp; system.Protein.chainA.itp and
On 11/4/13 1:29 PM, Stephanie Teich-McGoldrick wrote:
Dear all,
I am using gromacs 4.6.3 with a triclinic box. Based on the manual and mail
list, it is my understanding that the default box shape in gromacs in a
triclinic box. Can I assume that all the analysis tools also work for a
triclinic
Thanks Joao Henriques for helping me with the steps.
On Nov 4, 2013 3:18 PM, João Henriques joao.henriques.32...@gmail.com
wrote:
Hello Archana,
I'm also toying with a TFE-water system, therefore I am also a newbie. This
is what I am doing, I hope it helps:
1) Since I'm using G54A7 I
Dear Mark,
Sorry for replying to an older thread. We are trying to perform implicit
solvent simulations of protein G with CHARMM27 in gromacs. We are trying
to trouble shoot why the protein unfolds after already 2 ns of dynamics.
We use simulated annealing for the heating with 1 fs time step.
Hi Justin
Thanks for your response. Here are the files you asked for. They are all text
files. I am still attempting to fix this, but am still getting the error I
described no matter what I have done so far.
Thanks again,
Stevegrompp -f pr.mdp -n pr.ndx -c prbox.pdb -p system.top -o pr.tpr
--
On 11/4/13 3:03 PM, Steve Seibold wrote:
Hi Justin
Thanks for your response. Here are the files you asked for. They are all text
files. I am still attempting to fix this, but am still getting the error I
described no matter what I have done so far.
The list does not accept attachments,
On 11/4/13 2:25 PM, Gianluca Interlandi wrote:
Dear Mark,
Sorry for replying to an older thread. We are trying to perform implicit solvent
simulations of protein G with CHARMM27 in gromacs. We are trying to trouble
shoot why the protein unfolds after already 2 ns of dynamics. We use simulated
Hi gmx users,
I want to simulate ionomer is mixed solution of water and ethanol using gromos
force field.
I tired to follow the steps suggested on gromacs website, which are:
1- Determine the number of co-solvent molecules necessary, given the box
dimensions of your system.
2- Generate a
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
You have a number of molecules, you know what those molecules are, you can
calculate their mass, you know the volume, therefore you can calculate a
density. For the average for entire simulation, simply pass the water.xvg file
to g_analyze
There is all the information you require right there
On 11/4/13 5:25 PM, Ehsan Sadeghi wrote:
Hi gmx users,
I want to simulate ionomer is mixed solution of water and ethanol using gromos
force field.
I tired to follow the steps suggested on gromacs website, which are:
1- Determine the number of co-solvent molecules necessary, given the box
Hi Justin,
We are using infinite cutoffs (all vs all). Here is the mdp file for the
heating (please note that -DPOSRES is commented out) and the time step is
1 fs:
; VARIOUS PREPROCESSING OPTIONS =
title=
cpp = /lib/cpp
include =
Hi,
I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having
32 processors (cpu). But while running the nvt equilibration step, it uses
only 1 cpu and the others remain idle. I have complied the Gromacs using
enable-mpi option. How can make the mdrun use all the 32 processors ??
Hi,
I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having
32 processors (cpu). But while running the nvt equilibration step, it uses
only 1 cpu and the others remain idle. I have complied the Gromacs using
enable-mpi option. How can make the mdrun use all the 32 processors ??
Dear all
I would like to carry out unfolding simulations of my dimeric protein and
would like to know which is the better force field to work with out of
gromos 96 43 or 53? Also, is gromos 96 43a1 force field redundant?
When I searched the previous archive, I could see similar question was
Dear All,
I have an problem related to jumping trajectory. In my MD
run, there is a receptor molecule which is binding with an halogen anion in
water solvent. In the original trajectory, the binding between them looks
fine but jumping present. To remove the jumping of the system from
Dear Gromacs Users!
I'd like to compile lattest 4.6 Gromacs with native GPU supporting on my i7
cpu with dual GeForces Titans gpu mounted. With this config I'd like to
perform simulations using cpu as well as both gpus simultaneously.
What flags besides
cmake .. -DGMX_GPU=ON
all-bonds and none work, so I assume, as alternating between these settings speeds up the EM. However, I always see the protein move around in the box after centering, so just re-center after reaching pressure and temp stability before the extended pre-run equilibration with set restraints (which
That last procedure works. I really appreciate your help. The only other
question I have is related to the selection process. Is there a way to
select the oxygen atoms of water within a certain distance of a molecule, as
well as the corresponding hydrogen atoms on the water molecule? Right
On 11/3/13 6:20 AM, kiana moghaddam wrote:
Dear Justin
Further to your previous email, I want to calculate free energy for DNA-ligand
interaction. According to your answer, for more sensitive calculations like free
energy simulations and normal modes, emtolshould be lower than 1. As
I
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