st regards,
Peng
On Mon, Oct 4, 2010 at 7:55 PM, Mark Abraham wrote:
>
>
> - Original Message -
> From: 吴鹏
> Date: Tuesday, October 5, 2010 3:24
> Subject: [gmx-users] Can I customize Gromacs (e.g., on-fly-analysis) with
> multi-threading enabled?
> To: Discussion
Dear All:
I am trying to do trajectory analysis on-the-fly and encountered some
difficulty.
What did I do:
I inserted a small piece of code into "md.c" to READ the position of
atoms and do some simple analysis. In the GMX3.2, my code works fine.
The problem:
In GMX4.5.1, my code works only if I
Hello GMX users,
I want to reproduce the shifted VDW force done by Gromacs but the
efforts is in vain. The result given by Gromacs was slightly
different(1*10^-3 depends on the atoms distance) form the result got
from the way suggested by the manual.
I tested a case in which there are two atoms w
Hi Mark,
What you said reminds me to think deeply about my speculation. Thanks for
your remind and I hope to discuss it with you when I get some ideas on that.
Peng Wu
On Tue, Oct 13, 2009 at 10:02 AM, Mark Abraham wrote:
> 吴鹏 wrote:
>
>> Hi Mark,
>>
>> Haha. Yes,
Hi Mark,
Haha. Yes, your words is right. My objective is to study the interaction
between ions and walls. I think the ions may be attached in the wall so the
velocity getten from MD simulation is always bigger than the continuum
theory's prediction. So I want to build a simulation on which ion can
Hi GMX users,
I am doing a modified simulation which requires to eliminate an interaction
at certain direction while remain the interaction at other directions. Since
the itp files contain the C6 C12 of the interaction, it is impossible to
only remain the interaction a one direction while eliminat
Use editconf to change gro file type to pdb file.
On Wed, Sep 9, 2009 at 8:29 PM, Amit Choubey wrote:
> hi everyone,
> I have a pdb file of my system and i want it to be fed into the GROMACS
> software. I have a new force field for the simulation and i have made the
> .top file manually which in
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