Hi to all.
i had installed gromacs on wondows platform gromacs using cygwin by follow the
advices in the gromacs istallation page.
When i start the software cygwin, i type cd Gromacs to go inside the Gromacs
forlder, and foward i type
pdb2gmx -f namefile.pdb
i got the message:
-bash
hello justin
Can you please tell me how will i solvate my system.
which command will i use and what will be my input and output file.
Thanks for your help
Anurag dobhal
On Sun, Sep 28, 2014 at 6:58 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/28/14 9:14 AM, Anurag Dobhal wrote:
Hey
Hi,
Did you try
http://www.gromacs.org/Documentation/Installation_Instructions#getting-access-to-gromacs-after-installation
?
Mark
On Mon, Sep 29, 2014 at 9:57 AM, marcello cammarata mstaxmarce...@yahoo.it
wrote:
Hi to all.
i had installed gromacs on wondows platform gromacs using cygwin by
Dear list,
I am a little bit confused regarding the preparation needed to use the AMBER FF
in GROMACS 5.0.1. I have a simple PDB file of a protein and I use this as
input to pdb2gmx. I selected the AMBER FF during the creation process:
gmx_mpi pdb2gmx -f protein.pdb -o protein_processed.gro
Dear all,I have been using the SWM4-NDP water model that works well with CHARMM27 force field.The force field (most recent version) was obtained from virtualchemistry, and consists of polarisable ions and the SWM4-NDP water model from Lamoureux et al.The water on graphene (energy minimisation and
On 9/29/14 4:44 AM, Anurag Dobhal wrote:
hello justin
Can you please tell me how will i solvate my system.
which command will i use and what will be my input and output file.
Consult a basic tutorial for this information. The membrane protein tutorial
assumes the user is already familiar
On 9/29/14 5:58 AM, Ebert Maximilian wrote:
Dear list,
I am a little bit confused regarding the preparation needed to use the AMBER FF
in GROMACS 5.0.1. I have a simple PDB file of a protein and I use this as
input to pdb2gmx. I selected the AMBER FF during the creation process:
gmx_mpi
I am wondering if anyone tested the performance of new GTX 980 and 970 cards
and compared to 780/780Ti/Titan using the input systems given here:
http://www.gromacs.org/GPU_acceleration Thank you.
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Gromacs Users mailing list
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On 9/29/14 8:01 AM, Kester Wong wrote:
Dear all,
I have been using the SWM4-NDP water model that works well with CHARMM27 force
field.
Time out. SWM4-NDP is a polarizable water model, and CHARMM27 is an additive
force field. The two are not compatible. If you're using them together,
On 29.09.2014 14:31, Pappu Kumar wrote:
I am wondering if anyone tested the performance of new GTX 980 and 970 cards
and compared to 780/780Ti/Titan using the input systems given here
As long as I don't have a card, I can only guess.
But: until the appearance of reasonable benchmarks, you
Hi,
is this the only output?
Don’t you get a perf.out file that lists which settings are optimal?
What exactly was the command line you used?
Carsten
On 29 Sep 2014, at 15:01, Ebert Maximilian m.eb...@umontreal.ca wrote:
Hi,
I just tried that and I got the following error message
Dear gromacs usres,
I have run the umbrella sampling with the help of tutorial of justinIn
my system rna is binding with gold nanoparticle...to find out the binding
energy, i run the umbrella sampling by pulling one end of the siRNA untill
it unbind from gold nanoparticle. The snap shots
On Mon, Sep 29, 2014 at 2:46 PM, Mirco Wahab
mirco.wa...@chemie.tu-freiberg.de wrote:
On 29.09.2014 14:31, Pappu Kumar wrote:
I am wondering if anyone tested the performance of new GTX 980 and 970
cards and compared to 780/780Ti/Titan using the input systems given here
As long as I don't
Hi,
I see where the problem is.
There is an initial check in g_tune_pme to make sure that parallel
runs can be executed at all. This is being run with the automatic
number of PME-only ranks, which is 11 for your input file.
Unfortunately, this results in 37 PP ranks, for which no domain
Thank you very much for your help. This answered my questions.
I wish you a great day,
Max
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: Montag, 29. September 2014
Thank you for your info. I am planning to buy a computer with the following
configuration:
Intel 5820K
Corsair H100i Hydro Cooling Performance
MSI X99 SLI Plus
Fractal Design R4
Seasonic X 1050W
I am wondering if it would be a good idea to go for 3x GTX 970 instead of 2x
GTX 980 since the
Hi,
It can't be fixed, because there is no surefire way to run an arbitrary tpr
on arbitrary number of ranks, regardless of how you guess -npme might
succeed. We should just make the check optional, instead of being a deal
breaker.
Mark
On Sep 29, 2014 4:35 PM, Carsten Kutzner ckut...@gwdg.de
Hi,
That seems suitable.
Mark
On Mon, Sep 29, 2014 at 6:32 PM, Carsten Kutzner ckut...@gwdg.de wrote:
Hi,
On 29 Sep 2014, at 18:17, Mark Abraham mark.j.abra...@gmail.com wrote:
Hi,
It can't be fixed, because there is no surefire way to run an arbitrary
tpr
on arbitrary number of
Hi,
On 29 Sep 2014, at 18:17, Mark Abraham mark.j.abra...@gmail.com wrote:
Hi,
It can't be fixed, because there is no surefire way to run an arbitrary tpr
on arbitrary number of ranks, regardless of how you guess -npme might
succeed.
What about making this check on two ranks always,
Hi!
I'm trying to run g_tune_pme on a case with verlet lists, but i get
complaints from mdrun that
With Verlet lists rcoulomb and rvdw should be identical
even with -scalevdw.
Using 4.6.5
g_tune_pme -r 3 -min 0.1 -rmin 0.7 -rmax 1.1 -scalevdw -ntpr 10 -s case.tpr
Is this a known problem or
On 29 Sep 2014, at 19:10, Åke Sandgren ake.sandg...@hpc2n.umu.se wrote:
Hi!
I'm trying to run g_tune_pme on a case with verlet lists, but i get
complaints from mdrun that
“With Verlet lists rcoulomb and rvdw should be identical”
But does mdrun like your input file?
Carsten
even with
On 29 Sep 2014, at 18:40, Mark Abraham mark.j.abra...@gmail.com wrote:
Hi,
That seems suitable.
Oh, it just occurred to me that on systems that use the Load Leveler,
we have no means of specifying the number of MPI ranks on the command line,
since ‘poe’ has no switch for that.
So at least
Hi All,
Does anybody know what the uncertainty or error is for the QHA and/or
Schlitter calculations for configurational entropy in gmx_anaeig?
Daniel
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*
Hi,
On 29 Sep 2014, at 16:27, Szilárd Páll pall.szil...@gmail.com wrote:
On Mon, Sep 29, 2014 at 2:46 PM, Mirco Wahab
mirco.wa...@chemie.tu-freiberg.de wrote:
On 29.09.2014 14:31, Pappu Kumar wrote:
I am wondering if anyone tested the performance of new GTX 980 and 970
cards and compared
On 09/29/2014 07:17 PM, Carsten Kutzner wrote:
On 29 Sep 2014, at 19:10, Åke Sandgren ake.sandg...@hpc2n.umu.se wrote:
Hi!
I'm trying to run g_tune_pme on a case with verlet lists, but i get complaints
from mdrun that
“With Verlet lists rcoulomb and rvdw should be identical”
But does mdrun
On Mon, Sep 29, 2014 at 7:32 PM, Carsten Kutzner ckut...@gwdg.de wrote:
Hi,
On 29 Sep 2014, at 16:27, Szilárd Páll pall.szil...@gmail.com wrote:
On Mon, Sep 29, 2014 at 2:46 PM, Mirco Wahab
mirco.wa...@chemie.tu-freiberg.de wrote:
On 29.09.2014 14:31, Pappu Kumar wrote:
I am wondering if
On 9/29/14 10:09 AM, Sathish Kumar wrote:
Dear gromacs usres,
I have run the umbrella sampling with the help of tutorial of justinIn
my system rna is binding with gold nanoparticle...to find out the binding
energy i run the umbrella sampling using the space 0.2 nm and i got total
59
On 09/29/2014 09:54 PM, Mark Abraham wrote:
IIRC this was fixed in 4.6.6 (check release notes). You can use a more
recent g_tune_pme with older mdrun, in this case.
Typical :-)
Thanks.
--
Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
Internet: a...@hpc2n.umu.se Phone: +46 90
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