Hey together,
I am wondering when the stable version of 4.6 will be released. I am
using the prerelease version for basic NVT and NPT full atom simulations
for months now with great success and wonder what is missing for the
full release. I would be very grateful for some informations about the
cu
On 05/23/2012 02:16 PM, Justin A. Lemkul wrote:
>
>
> On 5/23/12 12:17 PM, SebastianWaltz wrote:
>> Hallo together,
>>
>> in the amino acid data base file (aminoacids.rtp) of the amber99sb-ildn
>> force field the H3 hydrogen of NPRO is missing.
>> Would b
Hallo together,
in the amino acid data base file (aminoacids.rtp) of the amber99sb-ildn
force field the H3 hydrogen of NPRO is missing.
Would be nice if someone could add the missing parameters or pose them.
Thanks a lot
Sebastian
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Hi all together,
I am testing the 4.6 dev version of gromacs with heterogeneous
acceleration (force field: amber99-ildn) on a 95 residue protein (all
atom model) in SPCE and run into major troubles using in the .mdp file
option constraints = hbonds with the default lincs parameters. The
system is
Dear all,
will the new version 4.6 work together with CUDA 4.2? Would be good to
know, since this is needed for the new NVIDIA Gemini cards with Kepler
technology.
Thanks,
Basti
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Dear Gromacs user,
I try to simulate the human Villin head peace HP35 in approx. 6000 water
molecules (spc) with the gromos ff ffG53a6. Using the 4.0.7 version the
NPT equilibration for 5ns with position restraint protein (lincs) atoms
and a integration step of 0.002 using the leap-frog integrator
On 03/23/2012 10:41 AM, francesco oteri wrote:
> Dear gromacs users,
> I have to perform REMD simulation, but since it is the first time I apply
> this tecnique I have a question regarding system equilibration.
> As far as I know, befaore starting the REMD each replica has to be
> equlibrated. The
Dear Gromacs user,
I am searching for the GROMOS (best would ffG53a5) forcefield parameters
of the rather rarely used amino acid AZIDOHOMOALANINE (C4 H8 N4 O2). The
residue looks like:
http://www.chembase.com/cbid_147480.htm
Every suggestion is very welcome since it can avoid doing the
parametri
Dear Gromacs user,
since a few days we try to get the heterogeneous parallelization on a
Dell blade server with Tesla M2090 GPUs to work using the worksheet on
the page:
http://www.gromacs.org/Documentation/Acceleration_and_parallelization
we only get the OpenMM pure GPU version with mdrun-gpu r
Hallo Development Team,
since NVIDIA is working on the release of the new Kepler technology
build manly for single precession calculation, it is interesting what
performance increase is expected for GROMACS 4.6 with such cards
compared to FERMI cards like the M2070.
Is their a reason why such card
Hi all,
I try to reproduce the results from g_angle using my own c++ code. Using
the formula
θ=acos(r_ij * r_kj/|r_ij||r_kj|)
with the acos from the cmath library, I obtain an angle which is always
~5% larger when the angel calculated by g_angle.
Does g_angle use the same formula or does it calc
On 10/04/2011 09:48 PM, Taylor Kaplan wrote:
> Hi Gromac Users,
>
> I stupidly overwritten my .edr file, but my .traj file is still intact. Is
> it possible to use my traj file to recover my energy file. I also have my tpr
> file which is also in one piece.
>
>
> Thanks,
>
> Taylor
>
Hi Taylor
Hi,
in the GROMACS implementation of REM the trajectories are exchanged not
the temperatures. The temperatures are kept constant. As well as the
description of the Okamoto paper cited by GROMACS
Basti
On 09/18/2011 01:35 PM, michael zhenin wrote:
> Hi All,
>
> I have few questions regarding REM
Hallo all together,
I am working on a system of a small peptide solvated in CHCl3.
I want to obtain the forces on the peptide atoms induced by the
solvent. For this I used the rerun option of mdrun_d. I did it now in
two ways:
1st: using trjconv to get the pure peptide trajectory. When using the
Dear all,
I want to calculate the force on each protein atom induced by the SPC
solvent. Therefore I use the mdrun -rerun option and add to the .mdp
file the line
energygrps = Protein SOL
If I compare afterwards the total force and the force of the solvent
written to the trr file I get
On 05/11/2011 05:20 AM, Mark Abraham wrote:
> On 05/11/2011 02:32 AM, SebastianWaltz wrote:
>> Dear GROMACS User,
>>
>> I'm running a REMD MD of 32 replicas. It worked for the first few
>> replica exchanges. After 30ps again two replicas were exchanged and I
>&
Dear GROMACS User,
I'm running a REMD MD of 32 replicas. It worked for the first few
replica exchanges. After 30ps again two replicas were exchanged and I
received the Error:
x particles communicated to PME node y are more than a cell length out
of the domain decomposition cell of their charge gro
Hi Mark,
On 05/10/2011 11:34 AM, Mark Abraham wrote:
> On 10/05/2011 5:36 PM, SebastianWaltz wrote:
>> Dear GROMACS users,
>>
>> I wonder if it is not possible to use more than 1 core (according to the
>> manual) for each replica using GROMACS 4.0.x?
>
> You can u
Dear GROMACS users,
I wonder if it is not possible to use more than 1 core (according to the
manual) for each replica using GROMACS 4.0.x?
In the manual is written that the number of cores defined by the -np
option of mpirun has to be the same as the number of replicas.
Thanks
Sebastian
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g
Dear gromacs user,
I have some problems getting a simulation running on a tesla T10 with
CUDA driver version 3.20 running.
My .mdp file looks like:
;
title= ttt
cpp= /lib/cpp
include = -I../top
constraints = none
;define
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