[gmx-users] Energy minimization problem in Choline Chloride+Urea mixture in Gromacs

[Christopher Neale]

Can you simulate a single molecule of choline in vacuum without it crashing? What about urea?

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Suman Das <sumandas212 at gmail.com>
Sent: 02 January 2015 11:21
To: gmx-users at gromacs.org
Subject: [gmx-users] Energy minimization problem in Choline Chloride+Urea       mixture in Gromacs

Hi,
 I am trying to simulate a mixture of Choline Chloride+Urea mixture with
33:67 ratio at 298 K. I have taken the force field of choline from this
paper :http://pubs.acs.org/doi/full/10.1021/jp404619x
<https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Fjp404619x>,
chloride from http://pubs.acs.org/doi/full/10.1021/jp063901o
<https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Fjp063901o>
and urea from http://pubs.acs.org/doi/full/10.1021/jp030534x
<https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Fjp030534x>.
During the minimization process Fmax < 200 but potential energy was quite
high~5.4465270e+04. And finally the simulation crushes.  I have used this
force field of urea previously which matches well with experimental data.
So I have tried with another force field of choline (
http://pubs.acs.org/doi/full/10.1021/jp301270y
<https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Fjp301270y>)
but exactly the same thing happens. I have also tried the freeze group
option. But the result is same. I built the box using packmol. I took the
initial box length 5nm.

regards,
Suman
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