Hi Sir,
Is it possible to run an REMD simulation having 16 replicas in a
cluster(group of cpu) having 8 nodes. Here each node have 8 processors.
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Dear GMXers,
With Gromacs 4.6.2 I was running REMD with 144 replicas. Replicas were
separate MPI jobs of course (OpenMPI 1.6.4). Each replica I run on 4
cores with OpenMP. There is Torque installed on the cluster build of
12-cores nodes, so I used the following script:
#!/bin/tcsh -f
#PBS -S
Dear GMXers,
With Gromacs 4.6.2 I was running REMD with 144 replicas. Replicas were
separate MPI jobs of course (OpenMPI 1.6.4). Each replica I run on 4
cores with OpenMP. There is Torque installed on the cluster build of
12-cores nodes, so I used the following script:
#!/bin/tcsh -f
#PBS -S
On 7/11/13 6:41 PM, Neha wrote:
The .cpt file stores information related to output frequency. The existing
.cpt
file designates output every X steps, while the new .tpr file specifies
output
every Y steps, and X != Y, so mdrun complains. I'm assuming mdrun aborts at
that point? Have you tr
The .cpt file stores information related to output frequency. The existing
.cpt
file designates output every X steps, while the new .tpr file specifies
output
every Y steps, and X != Y, so mdrun complains. I'm assuming mdrun aborts at
that point? Have you tried with -noappend?
Hi,
So this
On 7/11/13 5:10 PM, Shima Arasteh wrote:
Thanks for your reply.
But when I don't understand why these extra lines are needed to set when are
not advantageous practically! :-(
There's nothing "extra." Everything here has a functional purpose.
-Justin
Sincerely,
Shima
- Original M
Thanks for your reply.
But when I don't understand why these extra lines are needed to set when are
not advantageous practically! :-(
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Friday, July 12, 2013 1:3
On 7/11/13 4:21 PM, Shima Arasteh wrote:
Hi,
I want to run Umbrella Sampling on my system. In initial configurations, an ion
is located in center of the window.
Some mdp file settings for running US, as I found in US tutorial are :
; Pull code
pull= umbrella
pull_geometry = dist
On 7/11/13 3:14 PM, Neha wrote:
Hi everybody,
I started changing init-step. Now I seem to have another problem. When I go
to switch to another 'block' it tells me that my input and checkpoint states
are not identical when I use mdrun the second time. I am not sure how they
can be any different
Dear users,
I ran a "common MD simulation" of a solvated protein and, from the
full .trr, I extracted only the protein trajectory with trjconv, no solvent
nor ions. Similarly, I used the same original .tpr with tpbconv to get a
.tpr which corresponds only to the protein. I used mdrun -rerun w
Hi,
I want to run Umbrella Sampling on my system. In initial configurations, an ion
is located in center of the window.
Some mdp file settings for running US, as I found in US tutorial are :
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start
Hi everybody,
I started changing init-step. Now I seem to have another problem. When I go
to switch to another 'block' it tells me that my input and checkpoint states
are not identical when I use mdrun the second time. I am not sure how they
can be any different as I only have one .cpt file in the
if you prepare a separate ITP for each solvent, you will save some nerves
in the long term
Dr. Vitaly V. Chaban
On Thu, Jul 11, 2013 at 7:14 PM, Justin Lemkul wrote:
>
>
> On 7/11/13 8:59 AM, Shima Arasteh wrote:
>
>> Dear all,
>>
>> I see cyclohexane parameters in top & par CGenFF files
On 7/11/13 11:47 AM, juganta wrote:
Thanks Justin for your information. But I got those lines in /gromacs
4.5.5/top/tip3p.itp --
#ifdef _FF_GROMACS
#include "gmx.ff/tip3p.itp"
#endif
#ifdef _FF_GROMOS96
#include "gromos43a1.ff/tip3p.itp"
#endif
#ifdef _FF_OPLS
#include "oplsaa.ff/tip3p.itp"
#e
On 7/11/13 8:59 AM, Shima Arasteh wrote:
Dear all,
I see cyclohexane parameters in top & par CGenFF files. Would it be correct if
I add this molecule to the rtp file in charmm and then use it as a solvent rather
than for example water?
The .rtp mechanism is generally used for building bloc
Hi all,
If my understanding is correct, GROMACS parallelization and acceleration
page indicates AVX2 SIMD intrinsics can offer a speed boost on a Haswell
CPU. I was wondering how much performance gain we can expect from it. In
another word, what's the approximate speed increase if we run a simulat
Thanks Justin for your information. But I got those lines in /gromacs
4.5.5/top/tip3p.itp --
#ifdef _FF_GROMACS
#include "gmx.ff/tip3p.itp"
#endif
#ifdef _FF_GROMOS96
#include "gromos43a1.ff/tip3p.itp"
#endif
#ifdef _FF_OPLS
#include "oplsaa.ff/tip3p.itp"
#endif
I thought I can use tip3p.itp wi
Hi Trayder,
Thank you for the suggestion. I will try the plugin soon.
Yes, I can play the two trajectories simultaneously, one with protein
disabled. In this way, I indeed can get a very good presentation of what is
happening. However, it's quite inconvenient to set Graphical
Representations in V
ok thank you very much. i will try and get back to u
regards
divya
On 11 July 2013 14:26, Dr. Vitaly Chaban wrote:
> Indeed.
>
>
> So, go to your main topology file and define a new atom type "Xe" under an
> appropriate section. Then just add sigma and epsilon in the non-bonded
> section and y
Dear all,
I see cyclohexane parameters in top & par CGenFF files. Would it be correct if
I add this molecule to the rtp file in charmm and then use it as a solvent
rather than for example water?
Generally, how is it possible to add a new solvent to the charmm ff simulations?
Thanks in advance,
I have the same feeling, thank you. But in general mass can influence the
equilibrium property so I guess yes.
Steven
On Thu, Jul 11, 2013 at 1:27 PM, Justin Lemkul wrote:
>
>
> On 7/11/13 8:17 AM, Steven Neumann wrote:
>
>> Thank you. Another question: Does RDF depends on the mass of the atom
On 7/11/13 8:17 AM, Steven Neumann wrote:
Thank you. Another question: Does RDF depends on the mass of the atom? On
the one hand it gives different value of the force in equation of motion
but on the other hand velocities are rescaled with a thermostat.
My impression would be that the masses
Indeed.
So, go to your main topology file and define a new atom type "Xe" under an
appropriate section. Then just add sigma and epsilon in the non-bonded
section and you are ready to explore the binding.
Dr. Vitaly V. Chaban
On Wed, Jul 10, 2013 at 12:04 PM, Divya Sunil wrote:
> ya.. but t
Thank you. Another question: Does RDF depends on the mass of the atom? On
the one hand it gives different value of the force in equation of motion
but on the other hand velocities are rescaled with a thermostat.
Steven
On Thu, Jul 11, 2013 at 12:57 PM, Justin Lemkul wrote:
>
>
> On 7/11/13 7:5
On 7/11/13 7:54 AM, Steven Neumann wrote:
Dear Users,
Can you please write me where gromacs does read the mass of each atom: Is
that the [atoms] under [moleculetype] or from [atomtypes] ? I wish to
assign different mass for two different beads of the same type in my
topology.
It is taken fr
Dear Users,
Can you please write me where gromacs does read the mass of each atom: Is
that the [atoms] under [moleculetype] or from [atomtypes] ? I wish to
assign different mass for two different beads of the same type in my
topology.
Steven
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FYI: The MKL FFT has been shown to be up to 30%+ slower than FFTW 3.3.
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Szilárd
On Thu, Jul 11, 2013 at 1:17 AM, Éric Germaneau wrote:
> I have the same feeling too but I'm not in charge of it unfortunately.
> Thank you, I appreciate.
>
>
> On 07/11/2013 07:15 AM, Mark Abraham wrote:
>>
>> No
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