On 7/13/17 9:16 AM, Sonia Milena Aguilera Segura wrote:
Message: 2
Date: Thu, 13 Jul 2017 08:56:14 -0400
From: Justin Lemkul
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling
Message-ID:
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> From: "gromacs org gmx-users-request"
>
> To: "gromacs org gmx-users"
> Sent: Thursday, July 13, 2017 2:58:39 PM
> Subject: gromacs.org_gmx-users Digest, Vol 159,
On 7/10/17 10:52 AM, Sonia Milena Aguilera Segura wrote:
Dear Justin,
Thank you for the answer. I changed the two parameters suggested in the mdp
file and I ran again a minimization, 200 ps NVT, 200 ps NPT, and 1 ns MD for
the two cases of the previous mail, and now I am getting densities
Dear Justin,
Thank you for the answer. I changed the two parameters suggested in the mdp
file and I ran again a minimization, 200 ps NVT, 200 ps NPT, and 1 ns MD for
the two cases of the previous mail, and now I am getting densities around 771
g/m3 which is slightly underestimated, but close
On 7/7/17 10:11 AM, Sonia Milena Aguilera Segura wrote:
Dear Justin,
Thank you very much for your answer. I tried both approaches: erasing the
dihedral from the topology (first approach) and modifying the ffbonded.itp as
described in the previous mail, without adding any improper (second
Dear Justin,
Thank you very much for your answer. I tried both approaches: erasing the
dihedral from the topology (first approach) and modifying the ffbonded.itp as
described in the previous mail, without adding any improper (second approach).
I ran a minimization, 200 ps NVT, 200 ps NPT, and
On 7/6/17 6:34 AM, Sonia Milena Aguilera Segura wrote:
Dear Justin,
Thank you for your reply. I went trough the CHARMM forum and I found this post
of 2007,
https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat=28545,
which basically underlines the same issues I am having. I read
Dear Justin,
Thank you for your reply. I went trough the CHARMM forum and I found this post
of 2007,
https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat=28545,
which basically underlines the same issues I am having. I read this post before
posting here, and this why I came with the