Liu Shiyong wrote:
Hi,
We have a protein with two chains A and B. We want to calculate the
interaction energy only.
Would you advise how to define the energy groups for the chains and how
to output the interaction
energy between chains A and B ?
Have a search of the mailing list archives,
Hi,
We have a protein with two chains A and B. We want to calculate the
interaction energy only.
Would you advise how to define the energy groups for the chains and how to
output the interaction
energy between chains A and B ?
--
Shiyong Liu
Postdoc
center for bioinformatics in the university o
Hi Bala,
My guess is you're running with position restraints on. Check the
manual. And while you're at it, google for "how to ask questions the
smart way".
Tsjerk
On Fri, Jan 16, 2009 at 3:00 PM, bala ms wrote:
> Hi
> I am new to Gromacs, I am using V3.3.3. I have run the MD simulation
> (
Hello,
Does anyone know of a script that can convert CNS topology files to Gromacs
format?
Thanks,
Candice Viddal
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friendli wrote:
> Dear all,
>
> When I performing mutation free energy calculation from Leu to Ala, I
> first turn off the charge on the side chain of Leu. As I read from the
> GMX archive, the dG/dl curve should be rather smooth for turning off the
> partial charge.
> In this step(charge off/on)
Hi,
The example lookup tables in the directory share/top,
table6-8.xvg
table6-9.xvg
table6-10.xvg
table6-11.xvg
table6-12.xvg,
are all identical. So, which of the vdw potentials is tabulated here?
Thanks,
Sam
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Hello,
I was running different simulations with the following pull code
1/
;---PULL CODE -
pull= umbrella
pull_geometry = direction
pull_group1 = r_535
pull_vec1 = 0.51 0.026 0.273
pull_k1 = 110
pull_rate1 = 0.002 ; nm/ps = 20 A/ns
Hi
I am new to Gromacs, I am using V3.3.3. I have run the MD simulation
(using explicit solvent) for 1ns for my protein of interest and also the
examples which has given in the Manual.
I am getting same kind of graph for the both proteins by plotting CA vs time.
The graph shows RMSD value l
No, David, I get no warnings at all. Is there a way to make warnings more
explicit ?
Thank you
-Himanshu
On Tue, 13 Jan 2009, gmx-users-requ...@gromacs.org wrote:
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> Date: Fri, 16 Jan 2009 09:06:43 +0100
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Inconsistent shifts Problem when using g_rdf
>
> Lin, Pohan wrote:
> > I am running NPT simulations by using Parrinello-Rahman pressure
> > coupling on Gromacs 3.3.3. My
Lin, Pohan wrote:
I am running NPT simulations by using Parrinello-Rahman pressure
coupling on Gromacs 3.3.3. My system contains epoxy and cross-linker
molecules. By modifying the topology file (add bond, angle, torsion
terms in topology), all the molecules are connected together to be an
hu
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