I am using 24 processors and it is same for all steps.
this is the command in use:
tpbconv_mpi -f run.trr -s run.tpr -e run.edr -extend 1000 -o ext_11
nohup /opt/ScaleMP/mpich2/1.0.8/bin/mpirun -machinefile $PBS_NODEFILE -np 24
/opt/gromacs4/bin/mdrun_mpi -v -deffnm ext_11
--
On 19/08/2011 5:07 PM, Anupam Nath Jha wrote:
Is it the problem with the gromacs?
Probably not. Assuming you have kept everything else constant, it is likely that
other activity on the machine or file system is delaying you somehow.
This is still likely to be true. Other activity (other user
Hi,
I have simulated a protein complex and now i would like to know the residing
water molecules between the protein complex. g_hbond and trjorder helps in
giving the number of hydrogen bonds and distance. but is this the residence
time calculation. please help me with this. there few posts given
On Tuesday, August 2, 2011 at 5:17 AM, Ravi Kumar Venkatraman
wrote:
> I have got some topology and parameter file
for some small organic molecules from swissparam in *.mol2 format.
> I am
trying to generate *.top, *.gro & *.itp files using topolbuild. But I
dont know how to do. So can anybody
Hello,
I am trying to use "-ter" with the pdb2gmx command, seems its not working
fine.
>pdb2gmx -f -o -ter
I also used "-inter" option, its not working.
I am using 4.5.4 version. any help would be greatly appreciated.
Regards,
vijay
--
gmx-users mailing listgmx-users@gromacs.org
http://l
Vijayaraj wrote:
Hello,
I am trying to use "-ter" with the pdb2gmx command, seems its not
working fine.
>pdb2gmx -f -o -ter
If this is your command line it is severely broken.
I also used "-inter" option, its not working.
Please define "not working." It's working fine for me.
I
Thank you so much, all.
Jae H. Park
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Szilárd Páll
Sent: Thursday, August 18, 2011 9:19 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] more than 100% CPU
It is tru
Sure Mark. If your interest is in patrolling the Gromacs mailing list, then
I'll leave you to it.
On Thu, Aug 18, 2011 at 9:40 PM, Mark Abraham wrote:
> On 19/08/2011 1:41 PM, Junior Nebeker wrote:
>
> Correct. Other people (who are new to this list) need your help, and
> unless their requests
On 20/08/2011 1:13 AM, Junior Nebeker wrote:
Sure Mark. If your interest is in patrolling the Gromacs mailing
list, then I'll leave you to it.
If you have something constructive to contribute, please do. Otherwise,
please don't.
Mark
--
gmx-users mailing listgmx-users@gromacs.org
http:/
Hi All,
I wanted to solicit some feedback on what I think may be a bug related to
periodicity handling and/or implicit solvent simulations. I ran some
simulations of a few model peptides (some helices, hairpins, etc) and I got what
I believed to be very inflated results for backbone hydrogen
"-ter" or "-inter" options of pdb2gmx are working fine with all force fields
except amber force field. I cant select the terminal groups when I use amber
ff, it directly goes through the generation of top files without asking any
options for terminal group selection. I just want to use the none opt
On 20/08/2011 1:26 AM, Justin A. Lemkul wrote:
Hi All,
I wanted to solicit some feedback on what I think may be a bug related
to periodicity handling and/or implicit solvent simulations. I ran
some simulations of a few model peptides (some helices, hairpins, etc)
and I got what I believed t
On 20/08/2011 1:27 AM, Vijayaraj wrote:
"-ter" or "-inter" options of pdb2gmx are working fine with all force
fields except amber force field. I cant select the terminal groups
when I use amber ff, it directly goes through the generation of top
files without asking any options for terminal grou
Mark Abraham wrote:
On 20/08/2011 1:26 AM, Justin A. Lemkul wrote:
Hi All,
I wanted to solicit some feedback on what I think may be a bug related
to periodicity handling and/or implicit solvent simulations. I ran
some simulations of a few model peptides (some helices, hairpins, etc)
and
Hello,
I run a 5ns simulation for a single glucose molecule in gas phase.
I tried to plot radial distribution function for O---H intramolecular
interactions using following command.
g_rdf -f 6.trr -s 6.tpr -n index -o
In rdf.xvg file there is no data.
Can you tell what could be the reason.
I
I have sent this email days ago, but I got no answer.
Hope someone would saw it this time.
Sorry for disturbing.
Dear all:
I am using gromacs-4.0.2_localpressure to calculate the local
pressure of my system.
I have a question.
When rerun the mdrun from gromacs-4.0.
Nilesh Dhumal wrote:
Hello,
I run a 5ns simulation for a single glucose molecule in gas phase.
I tried to plot radial distribution function for O---H intramolecular
interactions using following command.
g_rdf -f 6.trr -s 6.tpr -n index -o
In rdf.xvg file there is no data.
Can you tell what
On 20/08/2011 1:45 AM, Justin A. Lemkul wrote:
Mark Abraham wrote:
On 20/08/2011 1:26 AM, Justin A. Lemkul wrote:
Hi All,
I wanted to solicit some feedback on what I think may be a bug
related to periodicity handling and/or implicit solvent
simulations. I ran some simulations of a few mo
Hi all,
I have a small molecule with a part like:
CH1 --- CH1 --- S --- CH2 --- CH1
|
CH1
I first tried PRODRG, and it turned out PRODRG assigned bond, angle, and
dihedral parameters according what are already present in the
gromos53a6.ff/ffbonded.itp file. Since this f
On 20/08/2011 1:57 AM, Yun Shi wrote:
Hi all,
I have a small molecule with a part like:
CH1 --- CH1 --- S --- CH2 --- CH1
|
CH1
I first tried PRODRG, and it turned out PRODRG assigned bond, angle,
and dihedral parameters according what are already present in the
gro
during local pressure calculation.
>
>
> ** **
>
> Thanks for any reply.
>
> ** **
>
> Best wishes,
>
> KONG Xian
>
> Tsinghua, Beijing, China****
>
>
>
>
>
>
> __ Information from ESET NOD32 Antivirus, ver
On Fri, Aug 19, 2011 at 8:13 AM, Junior Nebeker wrote:
> Sure Mark. If your interest is in patrolling the Gromacs mailing list,
> then I'll leave you to it.
>
I think before you type your response you should consider that Mark has
helped several hundred times over this mailing list.
> On Thu,
What criterion does the grompp utility use to identify H-atoms when it
is requested in the MDP file to apply constraints=h-bonds? Thanks.
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
--
gmx-users mailing lis
On Fri, Aug 19, 2011 at 20:02, Dr. Vitaly V. Chaban wrote:
> What criterion does the grompp utility use to identify H-atoms when it
> is requested in the MDP file to apply constraints=h-bonds? Thanks.
Any atom name starting with H or h (so case-insensitive).
Cheers,
Bogdan
--
gmx-users mailing
Thanks! That's reasonable.
On Fri, Aug 19, 2011 at 2:31 PM, Bogdan Costescu wrote:
> On Fri, Aug 19, 2011 at 20:02, Dr. Vitaly V. Chaban
> wrote:
>> What criterion does the grompp utility use to identify H-atoms when it
>> is requested in the MDP file to apply constraints=h-bonds? Thanks.
>
>
Of course I know of Mark's contributions. However, one's contributions, big
or small, shouldn't excuse him/her from being rude to others. That's my
constructive feedback - take it or leave it.
On Fri, Aug 19, 2011 at 9:51 AM, Amit Choubey wrote:
>
>
> On Fri, Aug 19, 2011 at 8:13 AM, Junior Ne
Dear experts,
I am intending to calculate the equilibrium density of a pure hydrocarbon at
different pressures , at 425 K. The normal boiling point of the liquid is
around 350 K. For pressures below 100 bar densities I am getting from NPT is
in accurate. I start form a structure which is compresse
Dear Email Sender,
Thank you very much for contacting me! Unfortunately, I am not available in the
office at the moment and cannot respond to your email. I will be able to handle
your request starting again Monday, August 22, 2011.
For all questions about CloudBroker and the CloudBroker Platfor
Hi!
If I may ask, but what is the gromacs version that is planned on the roadmap
to begin to work with the newer version of openmm? Specially interested due
to ATI support
Regards
Jones
On Thu, Aug 18, 2011 at 10:01 PM, Szilárd Páll wrote:
> Hi,
>
> Gromacs 4.5.x works only with OpenMM 2.x. Yo
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