Hi,
I used umbrella sampling method to restrain the distance of two molecules at
several distances. Then I can use g_wham to get the free energy as a function
of the distance. Is there any way that I can get the free energy as a function
of another parameter? Thanks a lot.
Sincerely,
Qian
--
ce
> problems since your 2nd-D will rely on brute-force to converge,
> and worse: the umbrellas in 1D can force the sampling in the 2nd-
> D to surmount energy barriers that might be circumvented in
> unrestrained sampling.
>
> Chris.
>
> -- original message --
>
>
>
> PLEASE NOTE: this email outlines an *idea* of how to accomplish
> what you want. You must check the match for yourself.
>
> Chris.
>
> Qian Wang qwang at mail.uh.edu
> Sat Jul 30 18:05:33 CEST 2011
>
> * Previous message: [gmx-users] umbrella sampling
>
Hi,
I want to simulate two seperate peptids in one box. However, when I use pdb2gmx
to build the top file of this system, I found that gromacs thought there is
only one peptide because it added bond, angle and other energy terms between
the termius of these two peptides. Is there any way to pr
- Original Message -
From: "Justin A. Lemkul"
Date: Wednesday, October 13, 2010 2:08 am
Subject: Re: [gmx-users] top file for two seperate peptides
To: Discussion list for GROMACS users
>
>
> Qian Wang wrote:
> >Hi,
> > I want to simulate two seperate peptids in o
Hi,
It works. Thanks a lot.
Sincerely,
Qian
- Original Message -
From: "Justin A. Lemkul"
Date: Wednesday, October 13, 2010 2:28 am
Subject: Re: [gmx-users] top file for two seperate peptides
To: Gromacs Users' List
>
>
> Qian Wang wrote:
> >Hi,
&
Hi,
I want to test different values of cutoff for vdw. However, in the list someone
said cutoff = 0.9 for vdw was used for paramaterizing of Gromos force field,
other values would cause error, and also there was someone saying that cutoff
for vdw should be set to 1.4. Can someone make this que
Hi,
I want to use pulling code. But I do not quite sure the meaning of pull_rate.
User guide saies this is the rate of change of the reference position. So if I
set this value to 0.0001, does it mean the reference postion will move 0.0001
nm/ps ? If yes, how to define the moving direction? Gen
Hi,
I use Gromacs4.0.5 to run a 20 ns npt simulation in periodic boundary box. At
first I put peptide in the center of the box, then I write comm_mode = linear
in *mdp file. However, the peptide still moves out of the box and go through to
the other side of the box. Is there any method that ca
Hi,
I am using Gromacs 4.0.5 for umbrella sampling. I know that I can use g_wham to
calculate the free energy along the constrained distance. Is there a command in
Gromacs 4.0.5 that can calculates the average of any other obserble (for
example, potential energy) along the constrained distance
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