Dear,
-o MT.PnoH.xtc instad of xtc extenstion use pdb you will get pdb file.
And then load it in vmd or pymol u can see it
On Wed, Nov 21, 2012 at 10:24 PM, Rausch, Felix wrote:
> Hi.
>
> Try to load in a .gro file of your system first. After that, use the "load
> data into molecule" option to
On 11/21/12 9:56 PM, junfang.zh...@csiro.au wrote:
Dear GROMACS users
I am just wondering if you could help with transferring the GROMACS96 proper
dihetral parameters to the OPLS proper dihedral parameters or point me to some
references.
Gromos96 uses periodic dihedrals and OPLS uses Ryck
Can you re-compile with debugging symbols and obtain a full backtrace?
-Justin
On 11/21/12 11:58 AM, Emanuele Coccia wrote:
4.1.1 installed from binaries.
2012/11/21 Justin Lemkul
On 11/21/12 11:11 AM, Emanuele Coccia wrote:
Running your benchmark for the first time (dhfr-impl-1nm.benc
Dear GROMACS users
I am just wondering if you could help with transferring the GROMACS96 proper
dihetral parameters to the OPLS proper dihedral parameters or point me to some
references.
GROMACS96 dihedral:
OPLS dihedral:
My second question is if CO2 has been parameterised in GROMACS96 forc
Generating velocities from a new random seed is normally regarded as good
enough. By the time you equilibrate, the chaotic nature of MD starts to
work for you.
Mark
On Nov 21, 2012 1:04 PM, "Felipe Pineda, PhD"
wrote:
> So how would you repeat the (let be it converged) simulation from
> differen
Roland,
He explicitly stated that he is using 20da718 which is also from the
nbnxn_hybrid_acc branch.
Raf, as Roland said, get the release-4-6 ad try again!
There's an important thing to mention: your hardware configuration is
probably quite imbalanced and the default settings are certainly not
On Mon, Nov 19, 2012 at 6:25 PM, Szilárd Páll wrote:
> On Mon, Nov 19, 2012 at 4:09 PM, Thomas Evangelidis wrote:
>
>> Hi Szilárd,
>>
>> I compiled with the Intel compilers, not gcc. In case I am missing
>> something, these are the versions I have:
>>
>
> Indeed, I see it now in the log file. Let
Dear All,
I'd like to calculate the profile of a physical properties.
I used g_select command as below.
The value of i can be increased by an integer value. For example, the
command in the below
the z axis of the cell is divided the bins by the tickness of 2 nm. However
I'd make the tickness of e
Hi all,
I've read some earlier posts in the forum about replica exchange combined
with umbrella sampling but still not sure if the restrain potential defined
in the pull code will be included in the exchange criterion:
P(i<->j) = min (1, exp[ (beta_i-beta_j)*(U(Ri, Dj) + U(Rj,Di) - U(Ri,Di) -
U(R
Hi all,
I've read some earlier posts in the forum about replica exchange combined with
umbrella sampling but still not sure if the restrain potential defined in the
pull code will be included in the exchange criterion:
P(i<->j) = min (1, exp[ (beta_i-beta_j)*(U(Ri, Dj) + U(Rj,Di) - U(Ri,Di) -
4.1.1 installed from binaries.
2012/11/21 Justin Lemkul
>
>
> On 11/21/12 11:11 AM, Emanuele Coccia wrote:
>
>> Running your benchmark for the first time (dhfr-impl-1nm.bench) I have the
>> following message:
>>
>>
>> *Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single
>> precision
Hi.
Try to load in a .gro file of your system first. After that, use the "load data
into molecule" option to load in the .xtc.
-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im
Auftrag von shch406
Gesendet: Mittwoch, 21. November 201
On 11/21/12 11:45 AM, shch406 wrote:
Dear Gromacs users
To visualize my trajectory with VMD I applied trjconv to .xtc trajectory
file to eliminate water molecules and velocities remaining protein
coordinates only.
However, when I load this reduced file to VMD no image on screen appears,
nevert
On 11/21/12 11:11 AM, Emanuele Coccia wrote:
Running your benchmark for the first time (dhfr-impl-1nm.bench) I have the
following message:
*Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision)
*
*
*
*WARNING: OpenMM does not support leap-frog, will use velocity-verlet
i
Dear Gromacs users
To visualize my trajectory with VMD I applied trjconv to .xtc trajectory
file to eliminate water molecules and velocities remaining protein
coordinates only.
However, when I load this reduced file to VMD no image on screen appears,
nevertheless VMD have identified the file as a
Running your benchmark for the first time (dhfr-impl-1nm.bench) I have the
following message:
*Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision)
*
*
*
*WARNING: OpenMM does not support leap-frog, will use velocity-verlet
integrator.*
*
*
*
*
*WARNING: OpenMM supports onl
On 11/21/12 10:43 AM, Emanuele Coccia wrote:
Dear Support,
I have installed the version 4.5.5 of Gromacs, I have also installede
mdrun-gpu. I have a GeForce GTX 670 and CUDA toolkit 4.0; is this
environment compatible with Gromacs-GPU?
Likely. Are you having some issue getting mdrun to w
Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private Gromacs tutor.
On 11/21/12 9:50 AM, Kdead wrote:
Hello,
I have another problem after change the parameters.In the 43a1 force
fieldga_13 is 109.6 °，but my
ga_13 <90 ° after mdrun by Pymol softw
---
Florian Dommert
Dipl. Phys.
Institut für Computerphysik
Universität Stuttgart
Allmandring 3
D-70569 Stuttgart
Tel.: 0711-68563613
Fax: 0711-68563658
> -Ursprüngliche Nachricht-
> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] Im Auftrag von tarak
Thanks for the information Flo.
Before doing NPT I have already equilibrated my system by heating it
from 0K to 300K in 300 ps, then the pressure has reached to 1 bar. Now
while doing NPT I'm getting the excess pressure.
Is there any problem with the coupling constant ? I am checking it by
taking d
On 11/21/2012 11:41 AM, Ali Alizadeh wrote:
Dear Ivan
Thank you for your reply,
Dear Ali
please keep the discussion open to everybody...
In this way you will be sure that someone else will read and interact
with us, correcting me if I say something wrong to you..;-)
1- In your opinion, Can
So how would you repeat the (let be it converged) simulation from
different starting conditions in order to add that valuable statistics
you mention?
I think this was Albert's question
Felipe
On 11/21/2012 12:41 PM, Mark Abraham wrote:
If a simulation ensemble doesn't converge reliably over
If a simulation ensemble doesn't converge reliably over a given time scale,
then it's not converged over that time scale. Repeating it from different
starting conditions still adds valuable statistics, but can't be a
replicate. Independent replicated observations of the same phenomenon allow
you to
Dear Ali
the paper that you are citing is using a rigid TIP4P water model
As far as I know, emtol is relevant only for minimization or molecular
dynamics with shell particle or flexible constraints.
Therefore, as Justin told you, the emtol value should be irrelevant.
Concerning this paper,
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