Dear Eudes:
Thanks for working with me on this one! What you are getting is
actually what you are asking for in your .mdp file. You restrain the
Z-projection of the displacement, but do not affect the X and Y
components of the displacement with pull_dim = N N Y. If you want to
pull with s
4. PMF in vacuum and pull direction (chris.ne...@utoronto.ca)
>
>
>
> Message: 4
> Date: Tue, 08 Jun 2010 12:14:34 -0400
> From: chris.ne...@utoronto.ca
> Subject: [gmx-users] PMF in vacuum and pull direction
> To: gmx-users@gromacs.org
> Message-ID: <20100608121434.u6rhqhz400
ate1 = 0.001
pull_k1 = 1600
Message: 4
Date: Tue, 08 Jun 2010 08:05:23 -0400
From: chris.neale at utoronto.ca
Subject: [gmx-users] PMF in vacuum and pull direction
To: gmx-users at gromacs.org
Message-ID: <20100608080523.i6oo62he1wwc0wkg at webmail.utoronto.ca>
Content-Type: text/plain
im = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = BEN1
pull_group1 = BEN2
pull_vec1 = 0 0 1
pull_rate1 = 0.001
pull_k1 = 1600
> Message: 4
> Date: Tue, 08 Jun 2010 08:05:23 -0400
> From: chris.ne...@utoronto.ca
> Subject: [gmx-users] PMF in vacuum and pull direction
>
2010 12:12:03 -0400
From: chris.ne...@utoronto.ca
Subject: [gmx-users] PMF in vacuum
To: gmx-users@gromacs.org
Message-ID: <20100527121203.orb2sq228s4ow...@webmail.utoronto.ca>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
format="flowed"
Dear
man)
> 4. vibrational spectra of glucose (Nilesh Dhumal)
>
>
> --
>
> Message: 2
> Date: Thu, 27 May 2010 12:12:03 -0400
> From: chris.ne...@utoronto.ca
> Subject: [gmx-users] PMF in vacuum
> To: gmx-users@gromacs.org
> Message-ID: <20100
Dear Eudes:
To answer your pbc vs no-pbc question, I suggest that you use pbc=no
and set nstlist=0 rlist=0 rvdw=0 rcoulomb=0 so that you calculate all
interactions in direct space with no cutoffs.
## Major comments that you should still investigate
1. There is no need to use a virtual atom,
Dear Eudes:
Can you please elaborate on your description? What .mdp options are
you using? What exactly do your curves look like (you can post
pictures to photobucket or some other online service and link them
here)? If you suspect that you are doing something wrong, then we need
to under
Hi gmx-users,
I'm trying to simulate a umbrella sampling PMF between two benzene
molecules
in vacuum. My protocol is working fine, my histograms have good overlap and
the curves I have got are quite reasonable.
However I have noticed that some options in my .mdp file can significantly
change
the d
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