Dear all
I am involved in a project where the target systems are lipid bilayers
with and without different macromolecules embedded. In the past I did
quite a lot of MD simulations of membrane systems always removing the
COM motion of lipids and the solvent in separate groups. There are
Dear all,
I am doing a simulation of protein of my interest. I could run the simulation
following the lysozyme tutorial. I am using 2018 version for gromacs.
To start with, I ran the simulation for 1 ns. I want to run long simulation
though want to make sure that each trajectory files has a
rences between state.cpt and state_prev.cpt?
I am back to simulations after years, last I used was gromacs 3.x series.
Things are bit different now !
Thanks a lot for your help.
Best,
R
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Dear gromacs users,
I have been working on gromacs package for performing md simulations.
recently i have started using cluster with 2 nodes with 64 cores each.
I am eager to know whether a job run on 32 cores for few ns and later i
continue the same job on 64 cores (or vice versa), will show any
Hi;
I've already converted topology and coordinate files which were generated with
amber tools to .gro format. But now, when I want to add 100Mm NaCl to the
system I get this error:
Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file
'c6m1_GMX.top'
For more
Hi;
I've alreadyconverted the amber topology and coordinate files to gromacs
format.But when I want to start running theenergy minimization first by using
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code
Hi;
I've alreadyconverted the amber topology and coordinate files to gromacs
format.But when I want to start running theenergy minimization first by using
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code
Hi;
I've alreadyconverted the amber topology and coordinate files to gromacs
format.But when I want to start running theenergy minimization first by using
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code
Hi;I've alreadyconverted the amber topology and coordinate files to gromacs
format.But when I want to start running theenergy minimization first by using
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code
Hi;
I've used ff14sbamber force field to generate my system. As this force field
doesn'texist in gromacs, I generated the first structure of my system withamber
tools then I converted the topology and coordinate files intogromacs format by
using acpype. (In the amber tools I've added NaClto my
Hi;
I want to convert amber topology and coordinate files into gromacs topology
and coordinate file with the acpype command ( acpype -p FFF_AC.prmtop -x
FFF_AC.inpcrd ), but when I type it, I get this error: acpype: command not
found
I've done the procedure mentioned in the website:
Hi;
I want to use ff14SB Amberprotein force field. But it isn't included in the
gromacs force fields list.Is it possible to use this force field? How can I add
it in?Thank you, Mohammad.
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of the
present forcefields in gromacs.
Regards,-Maryam
On Sun, Aug 9, 2015 at 5:57 PM, mohammad r mohammad.r0...@yahoo.com wrote:
Hi;
I want to use ff14SB Amberprotein force field. But it isn't included in the
gromacs force fields list.Is it possible to use this force field? How can I add
Hi everybody;
I have a cubic box with a peptide in its center (the .gro file). Now I want to
add some lipids (e.g. 3 molecules)(I have the .gro and .top and .pdb files of
the lipid) to this box. But I don't know how to do it.I think that "gmx
insert-molecules" command will help, but again I
Hi everybody;
I have a cubic box with a peptide in its center (the .gro file). Now I want to
add some lipids (e.g. 3 molecules)(I have the .gro and .top and .pdb files of
the lipid) to this box. But I don't know how to do it.I think that "gmx
insert-molecules" command will help, but again I
Hi;
I tried to install GROMACS using "Installation guide for GROMACS 5.0.5" in the
gromacs.org, but I got an error after typing "cmake .. " line, then I tried
"sudo apt-get install gromacs" command, it installed the gromacs-4.6.5 but I
want the gromacs-5.0.5.
what should I do?
Thank you,
Hello everybody;
I want to install gromacs-5.0.5 in ubuntu-14.04 using the installation
instruction in the website "gromacs.org", but in the "cmake ..
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON" line I got this error:
-- No compatible CUDA toolkit found (v4.0+), disabling native GPU
Hello
I am running a series of FEP MD simulations using Gromacs 5.0.4, for each a
steepest descents minimization, NVT equil, NPT equil and production run,
all controlled by a central script. However, only about 50% of the runs get
through the NVT equilibration without crashing - crash error as
Hi everybody,
I want to convert the topology and coordinate files fromamber to gromacs
format. I used acpype bu it didn’t work properly (actually mysystem is
consisted of some lipids in a water-protein system but when I convertthe files
via acpype, the backbone is consisted of a mass
On Thu, Jun 16, 2016 at 2:32 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
> Hi,
>
> On Thu, Jun 16, 2016 at 9:30 AM Husen R <hus...@gmail.com> wrote:
>
> > Hi,
> >
> > Thank you for your reply !
> >
> > md_test.xtc is exist and writa
in the check
> that takes place when the checkpoint is read is not relevant to the
> problem.
>
> Mark
>
> On Thu, Jun 16, 2016 at 9:46 AM Husen R <hus...@gmail.com> wrote:
>
> > On Thu, Jun 16, 2016 at 2:32 PM, Mark Abraham <mark.j.abra...@gmail.com>
>
all your ranks/cores choosing to checkpoint at the same time.
> Pick a portable file format.
>
> Mark
>
> On Thu, Jun 23, 2016 at 4:15 AM Husen R <hus...@gmail.com> wrote:
>
> > Hi all,
> >
> > For academic purpose, I'm wondering how does checkpoint feature in
&
s per node:4
Logical cores per node:8
Hardware detected on host head-node (the node of MPI rank 0):
CPU info:
Vendor: GenuineIntel
Brand: Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected
doing.
>
> Mark
>
> On Thu, Jun 23, 2016 at 10:15 AM Husen R <hus...@gmail.com> wrote:
>
> > Hi,
> >
> > I still unable to find out the cause of the fatal error.
> > Previously, gromacs is installed in every nodes. That's the cause Build
> > time m
Hi Mark,
Thank you very much!
Regards,
Husen
On Thu, Jun 23, 2016 at 3:42 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
> Yes
>
> On Thu, Jun 23, 2016 at 9:54 AM Husen R <hus...@gmail.com> wrote:
>
> > Hi,
> >
> > Could you tell me the locat
Hi all,
For academic purpose, I'm wondering how does checkpoint feature in Gromacs
works ?
is there any resource/tutorial that I can learn ?
Thank you in advance,
Husen
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Hi all,
I got the following error message when I tried to restart gromacs
simulation from checkpoint file.
I restart the simulation using fewer nodes and processes, and also I
exclude one node using '--exclude=' option (in slurm) for experimental
purpose.
I'm sure fewer nodes and processes are
PROCESSES
= PID 6983 RUNNING AT head-node
= EXIT CODE: 1
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===
On Thu, Jun 16, 2016 at 11:48 AM, Husen R <hus...@gmail.com>
t tried to operate
> upon md_test.xtc, so perhaps you need to consider whether the file exists,
> is writable, etc.
>
> Mark
>
> On Thu, Jun 16, 2016 at 6:48 AM Husen R <hus...@gmail.com> wrote:
>
> > Hi all,
> >
> > I got the following error message when
Hi everybody,
I have the DMF pdb file and I want to import it to gromacs by pdb2gmx command,
but the residues are not included in none of the forcefields. can you please
help me figure this out?
Thank you, Mohammad.
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Hi,
I used the "gmx do_dssp" command to get the secondary structure of the protein
during the simulation but the resolution of the resulted .xpm file is very low.
how can I increase its resolution?
Thank you, Mohammad.
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Hi GROMACS users,
I have some questions: 1- Can I model a carbonnanotube (CNT)
conveying fluid in GROMACS subjected to a magnetic field?2- How can I
check the centerof mass velocity of my system?3- I want to calculate
volumeand water self diffusion coefficient
I changed and reduced the ratio but the xpm file was not changed at all.
On Sunday, February 14, 2016 5:05 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 2/14/16 1:54 AM, mohammad r wrote:
> Thank you Justin,
>
> I used xpm2ps command with below m2p file but
, 2016 6:31 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 2/15/16 1:31 AM, mohammad r wrote:
> I changed and reduced the ratio but the xpm file was not changed at all.
>
Unfortunately there's not much I can tell you here because this is rather
cryptic. It's illogical to get the
Hi gromacs users,
I've generatedinitial structure of my system by using ambertools (topology
andcoordinate files) and converted it to gromacs format (.gro and .top)by
parmed, but in topology file it doesn't refer to any forcefield.Does it make
any problem in the results or it is ok? Because
Thank you very much Justin
On Saturday, February 20, 2016 10:53 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 2/20/16 8:49 AM, mohammad r wrote:
> Hi Justin,
>
> Thank you for your answer, I used grompp and it didn't give me error. I've
> attached a topology file
Hi everybody,
Is it correct to say the potential energy after energyminimization should be
negative and in the order of 105-106 ?according to gromacs tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html
Thank you, Mohammad.
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Gromacs Users
Thank you Justin,
do you know how I can find or modify the center of mass velocity of my system?
On Sunday, February 21, 2016 11:50 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 2/21/16 3:15 PM, mohammad r wrote:
> Hi everybody,
>
>
>
> Is it correct to say the p
edu>
wrote:
On 2/13/16 1:33 AM, mohammad r wrote:
> Hi,
> I used the "gmx do_dssp" command to get the secondary structure of the
> protein during the simulation but the resolution of the resulted .xpm file is
> very low. how can I increase its resolution?
You can a
Hi GROMACS users,
I have some questions:
1- Can I model a carbonnanotube (CNT) conveying fluid in GROMACS
subjected to a magnetic field?
2- How can I check the centerof mass velocity of my system?
3- I want to calculate volumeand water self diffusion
Thank you Justin for your help.
On Wednesday, March 9, 2016 6:38 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 3/9/16 1:42 AM, mohammad r wrote:
> Thank you Parham and Justin, Excuse me I have another question, in simulation
> of a water-peptide system, is it necessary
Lemkul <jalem...@vt.edu> wrote:
On 3/8/16 3:59 AM, mohammad r wrote:
> Thank you Parham
> You mean that it is not necessary to do QM/MM simulation?
>
The trivial task of adding ions to neutralize the net charge on the system
certainly does not require anything like
AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 3/30/16 2:17 AM, mohammad r wrote:
> Hi gromacs users,
>
>
>
> I want to do QMcalculation to my system. Can the PRODRG sitedo it (according
> to gromacs tutorial)? Or I should do it by using gromacsitself? By
Hi all,
Currently, I'm trying to run mdrun command in parallel.
the following is my batch script using Slurm as a resource manager:
=Batch Script==
#!/bin/bash
#SBATCH -J Eq1
#SBATCH -o eq1-%j.out
#SBATCH -A pro
#SBATCH -N 2
#SBATCH -n 16
gmx mdrun -deffnm
ption to
> use it the old way as well.
>
> Regards,
> James
>
>
> On 05/04/16 08:19, Husen R wrote:
>
>> Dear all,
>>
>> I already installed gromacs-5.1.2 succesfully with the following
>> instruction :
>>
>> tar xfz gromacs-5.1.2.tar.gz
>&g
cation ::: Website :::
FaceBook
On Tue, Mar 8, 2016 at 3:32 PM, mohammad r <mohammad.r0...@yahoo.com> wrote:
Hi everybody, I’ve generated a water-peptide system, now I want to neutralize
it. Is adding adequate number of ions sufficient for neutralizing process or I
should do QM/M
Hi everybody, I’ve generated a water-peptide system, now I want to neutralize
it. Is adding adequate number of ions sufficient for neutralizing process or I
should do QM/MM simulation for the this process? Thank you, Mohammad.
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Dear all,
I already installed gromacs-5.1.2 succesfully with the following
instruction :
tar xfz gromacs-5.1.2.tar.gz
cd gromacs-5.1.2
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC
However, after
Thank you very much Justin for your helpful answer.
On Thursday, March 31, 2016 3:40 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 3/31/16 12:19 AM, mohammad r wrote:
> Thank you Justin, I want to do QM calculationbefore running equilibration
> then run the MD simulation by
Hi gromacs users,
I want to do QMcalculation to my system. Can the PRODRG sitedo it (according to
gromacs tutorial)? Or I should do it by using gromacsitself? By the way I’ve
generated the initial coordinate and topology files inamber tools then convert
it to gromacs format by using parmed
Hi,
Thanks a lot !
I'll try it,..
Regards,
Husen
On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 4/24/16 12:04 AM, Husen R wrote:
>
>> Dear all,
>>
>> is there any complete documentation discussing checkpoint/restart in
>
: md_0_1.cpt and
md_0_1_prev.cpt
is this because of -deffnm option ?
I just want to make sure.
Regards,
Husen
On Tue, Apr 26, 2016 at 11:45 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
> Hi,
>
> On Tue, 26 Apr 2016 06:19 Husen R <hus...@gmail.com> wrote:
>
> >
--mail-user=hus...@gmail.com
#SBATCH --mail-type=begin
#SBATCH --mail-type=end
mpirun gmx_mpi mdrun -cpi md_0_1_prev.cpt -deffnm md_0_1
Thank you in advance
Regards,
Husen
On Sun, Apr 24, 2016 at 7:57 PM, Husen R <hus...@gmail.com> wrote:
> Hi,
>
> Thanks a lot !
> I'll try
Dear all,
is there any complete documentation discussing checkpoint/restart in
Gromacs-5.1.2 ?
I found this link that discuss checkpoint (
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) and
this link that discuss restart (
Hi GROMACS users,
I solved my proteinin a defined box of water. Now I want to add ions to
neutralize thesystem. But when I use “grompp -f ions.mdp -c solv.gro
-pgromacs.top -o ions.tpr” to generate the .tpr file I receive thiserror :
Fatal error:No such moleculetypeSOLFor more informationand
anual.gromacs.org/documentation/5.1.2/install-guide/index.html#portability-aspects
> >> > (These thoughts are common to earlier versions also.)
> >> >
> >> > Mark
> >> >
> >> >
> >> > Best wishes
> >> >> Jame
I use Gromacs-5.1.2 and SLURM-15.08.10 as a resource manager.
On Sat, May 14, 2016 at 7:53 AM, Husen R <hus...@gmail.com> wrote:
> Dear all
>
> Does simulation able to be restarted from checkpoint file with fewer nodes
> ?
> let's say, at the first time, I run simulation wit
Dear all
Does simulation able to be restarted from checkpoint file with fewer nodes ?
let's say, at the first time, I run simulation with 3 nodes. At running
time, one of those nodes is crashed and the simulation is terminated.
I want to restart that simulation immadiately based on checkpoint
Lemkul <jalem...@vt.edu> wrote:
>
>
> On 5/13/16 8:53 PM, Husen R wrote:
>
>> Dear all
>>
>> Does simulation able to be restarted from checkpoint file with fewer
>> nodes ?
>> let's say, at the first time, I run simulation with 3 nodes. A
, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 5/13/16 8:53 PM, Husen R wrote:
>
>> Dear all
>>
>> Does simulation able to be restarted from checkpoint file with fewer
>> nodes ?
>> let's say, at the first time, I run simulation with 3 nodes. A
Yes sir, even though its not working
On Sun, Apr 17, 2016 at 9:41 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 4/17/16 11:35 AM, REMYA R wrote:
>
>> Dear sir,
>>
>> I am getting error while running simulation of Protein-Ligand complex ,
>>
/complex_old/06_equil.html
)
Here below I am pasting some information from em.log
D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
av. #atoms communicated per step for force: 2 x 48020.5
R E A L C Y C L E A N D T I M E A C C O U N T I N G
Computing: Nodes
il.com>
wrote:
> Hi,
>
> Probably you haven't built gromacs with MPI support, else the name of the
> binary would be gmx_mpi. You can get that confirmed if you look further
> down the output .log files.
>
> Mark
>
> On Wed, 20 Apr 2016 10:09 Husen R <hus...@gmail.com>
gt;
wrote:
> Hi,
>
> Probably you haven't built gromacs with MPI support, else the name of the
> binary would be gmx_mpi. You can get that confirmed if you look further
> down the output .log files.
>
> Mark
>
> On Wed, 20 Apr 2016 10:09 Husen R <hus...@gmail.com>
Hi all,
I tried to run mdrun on more than one node using the command available in
this url
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html
.
The following is my sbatch job :
###SBATCH
#!/bin/bash
#SBATCH -J sim
#SBATCH -o
> Hi,
>
> Probably you haven't built gromacs with MPI support, else the name of the
> binary would be gmx_mpi. You can get that confirmed if you look further
> down the output .log files.
>
> Mark
>
> On Wed, 20 Apr 2016 10:09 Husen R <hus...@gmail.com> wrote:
>
ld all be along the lines of
>
> mpirun -np 2 gmx_mpi mdrun
>
> or
>
> mpirun -np 2 mdrun_mpi
>
> if the admins have done an mdrun-only installation.
>
> I'll fix that for future versions
>
> Mark
>
> On Wed, 20 Apr 2016 13:34 Husen R <hus...@gmail.com&g
Hi gromacs users,
After completing production run, I gave this command
gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red
However, I got error,
---
Program: gmx xpm2ps, VERSION 5.1.1
Source file:
: [gmx-users] gmx xpm2ps
On 3/31/17 11:27 AM, Kulkarni R wrote:
> Hi gromacs users,
>
>
> After completing production run, I gave this command
>
>
> gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red
>
>
> However, I got error,
>
>
> ---
Subject: Re: [gmx-users] gmx xpm2ps
"gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red" -> "gmx xpm2ps -f
hbmap.xpm -o hbplot.eps -rainbow red"
You have a blanck space between the "-" and the "o".
On Fri, Mar 31, 2017 at 5:52 PM Kulkarni R <alumniph
ynopsis gmx lie [-f [.edr>]] [-o [.xvg>]] [-nice ] [-b ] [-e ] [-dt ] [-[no]w]
[-xvg ] [-Elj ] [-Eqq ] [-Clj ] [-Cqq ] [-ligand ]
Curr Comput Aided Drug Des. 2015;11(3):237-44.
On Thursday, March 16, 2017 12:15 PM, Kulkarni R
<alumniphys...@hotmail.com> wrote:
Hi gromacs
Thanks
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Nikhil Maroli
Sent: Thursday, March 16, 2017 7:41 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re:
Hi gromacs users,
In order to calculate delta G (Gibbs free energy) for protein ligand binding,
what are the steps to be followed in Linear interaction energy?
Are there any tutorials for the same?
Thanks,
Kulkarni.R
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Hi gromacs users,
After protein ligand simulations, I want to do energy analysis.
How to interpret the following data properly? What books and papers should we
refer?
Energy AverageErr.Est. RMSDTot-Drift
Hi gromacs users,
How to install mmpbsa using cgywin?
I am using gromacs through cgywin.
Thanks,
Kulkarni.R
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I try to implement CLYFF in gromacs. I created ffbonded.itp,
ffnonbonded.itp, atomtype.atp, forcefield.doc, forcefield.itp and
molecule.rtp. I want to simulate Kaolinite, and I try to use pdb2gmx to
create a topology. My first question is that should I create any other
files?
Dear users,
I try to implement Clayff forcefield for Kaolinite. I created my force
field (I'm not sure about it), but gromacs couldn't find my force field in
the directory. Here is my forcefield.
ffnonbonded
[ atomtypes ]
; name mass chargeptype sigma eps
HW 1
Hi,
I want to calculate RDF of my organic molecule with a solvent.
What should be the duration of my simulation?
Is 100 ps enough?
Thanks,
Vidya.R
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*
list at
> gromacs.org_gmx-users-ow...@maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. TIP4P/ice pdb file (G R)
>
Dear All,
I would like to simulate water using TIP4P/ice potential. My question is
that how can I generate .gro file for this simulation?
I will use TIP4P/ice topology that is available in SklogWiki, but I cannot
understand how can I generate .gro file for this topology. Can I easily use
Hi gromacs users,
After getting the output from topolbuild, how to construct topology file
using opls forcefield?
Can anyone send useful links for the same?
Thanks,
Vidya.R
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Hi gromacs users,
How to compile ambconv extracted from ambconv.tgz?
Thanks,
Vidya R
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Hi,
How to get good (and fast) performance from mdrun through available 8
logical CPU cores?
When I gave,
gmx mdrun -ntmpi 2 -ntomp 4 -v -deffnm eq
It seems to be slow, much slower than
gmx mdrun -v -deffnm eq.
Can anyone help?
Thanks,
Vidya R
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Dear usres,
I try to write clayff forcefield, and I want to simulate Kaolinite. I have
some questions about it.
1) should I write clayff forcefield separately or modify one of the
forcefields in share/top?
2) The directory for clayff forcefield should be included ffbonded.itp,
ffnonbonded.itp,
Dear all,
I want to calculate the relaxation of pure water cell at room temperature
and at freezing point, monitoring its equilibration in volume and in
potential energy. I have 3 question: 1) Can I use packmol for my initial
configuration? if there is any other option,please tell me. 2) Can I
Dear all,
I want to calculate the relaxation of pure water cell at room temperature
and at freezing point, monitoring its equilibration in volume and in
potential energy. I have 3 question: 1) Can I use packmol for my initial
configuration? if there is any other option,please tell me. 2) Can I
Hi gromacs users,
In this command,
gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eql2
how to determine the value of pme..
I want to include -npme...
Please help
Thanks,
Vidya.R
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Hi gromacs users,
When i tried using,
gmx tune_pme -np 8 -s eql2.tpr -launch
Got this error..
How to fix it?
[compute-0-3.local:28193] [[20294,1],0] ORTE_ERROR_LOG: A message is
attempting to be sent to a process whose contact information is unknown in
file rml_oob_send.c at line 105
Hi gromacs users,
What is the difference between gmx mdrun and gmx tune_pme? Which is better
to use in a cluster (especially when we submit our jobs through qsub
command?)
Also, what is the purpose of -np option in gmx tune_pme? Can someone
elucidate?
Thanks,
Viday.R
--
Gromacs Users
My log file is provided in the link below
Can you please look into it and let me know why the error arises?
I am feeding my commands in SGE cluster. When I run it in my login node,
gmx mdrun -v -deffnm eql runs well
But, through qsub command, (with 8 processors) It says,
mpirun noticed that
https://drive.google.com/file/d/0BxGqxeGwTDLbLWJ5SExDblVhRFU
/view?usp=sharing=59be86ad
On Sun, Sep 17, 2017 at 6:35 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 9/17/17 1:22 AM, Vidya R wrote:
>
>> My log file is provided in the link below
>>
>> Ca
whatever quirks exist with SGE are unfortunately between you, its docs and
> your cluster's docs and admins :-(
>
> Mark
>
> On Sun, Sep 17, 2017 at 7:23 AM Vidya R <vidyadevi2...@gmail.com> wrote:
>
> > My log file is provided in the link below
> >
> > C
Dear All,
I want to create an index file and select some especial atoms in a surface.
My problem is that I have only one residue for the whole surface. How can I
select the atoms on the surface as a different groups in my index file?
Thank you in advance,
Golnaz
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Gromacs Users mailing list
*
in my
> index file, should I delete these atoms from surfaces groups. let me
> explain better. Now I have 2 groups in my index file Sol and
> Kaoli(surface). I should select some atoms from the Kaoli. So first I
> define the atoms that I want to select in a seperate group, then I should
> e
Hi,
When I give these two commands
gmx grompp -f mdp/min.mdp -o min -pp min -po min
gmx mdrun -deffnm min
I get this error.
What to do?
Reading file min.tpr, VERSION 5.0.2 (single precision)
tMPI error: tMPI Initialization error (in valid comm)
Thanks,
Vidya.R
--
Gromacs Users mailing
Hi,
I give these commands
PATH=$PATH:"/usr/local/gromacs/bin/"
export GMXLIB=/usr/local/gromacs/share/gromacs/top
export LD_LIBRARY_PATH=/usr/lib
export MPIRUN="/usr/mpi/pgi/openmpi-1.2.8/bin/mpirun"
export
use the
> C++ performance is very poor. We recommend latest gcc or intel.
>
> Otherwise, configure GROMACS so that it uses the wrapper compilers when
> buildling, e.g. cmake -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++
> etc. Organizing this stuff is their job.
>
> Ma
ted since.
> Since a rebuild is the way to investigate that, definitely update to at
> least the latest 5.0.x while you do it.
>
> Mark
>
> On Mon, Sep 11, 2017 at 3:36 PM Wes Barnett <w.barn...@columbia.edu>
> wrote:
>
> > On Mon, Sep 11, 2017 at
Hi gromacs users,
I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)
I want to download and install dssp tool.
How to proceed?
Thanks,
Vidya.R
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Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
*
mailed Maarten at "m.hekkel...@cmbi.ru.nl" but I'm not sure this
> email is active anymore. Hopefully it is, otherwise please let me know.
>
> Best regards,
> J
>
> On Tue, Dec 5, 2017 at 6:38 AM, Vidya R <vidyadevi2...@gmail.com> wrote:
>
> > Hi gro
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