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 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
raised
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 ??
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 =
;defi
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
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 i
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
-
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
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
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, nor
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
--
g
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.
Thanks Joao Henriques for helping me with the steps.
On Nov 4, 2013 3:18 PM, "João Henriques"
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 created a TFE.itp using GROMO
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
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
system.Protein.
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
--
gmx-users mailing listgmx-
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 ge
On Mon, Nov 4, 2013 at 12:01 PM, bharat gupta wrote:
> 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
>
These is no
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 wrote:
> Szilárd, thanks for suggestion!
>
> What kind of CPU optimisation should I t
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 o
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 wrote:
> Im not sure on the prices of these systems any more, they are getting dated
> so th
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
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
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 wrote:
>
>
> On 11/4/13 7:37 AM, Ankita Naithani wrote:
>
>> I do have the .mdp file. Main thing I was concerned about were detai
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
--
gmx-users mailing list
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 tha
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 wrote:
>
>
> On 11/4/13 7:14 AM, Ankita Naithani wrote:
>
>> Hi Ju
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,
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 12:
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 isn'
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
unde
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, ho
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 the
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
--
==
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
> That should be enough. You may want to use the -march (or equiv
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 ./configure
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,
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 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 ./configure
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.
> T
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 simu
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 wrote:
> Dear Gromacs Users!
>
> I'd like to compile lattest 4.6 Gromacs with native GPU supporting on my i7
> cpu w
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 molecules
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 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?. My
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
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