[gmx-users] Error In Umbrella sampling.
t.piggot at soton.ac.uk
Fri Apr 14 20:12:07 CEST 2017
I too also fairly frequently use the -maxwarn option for this message.
Perhaps it would be better off as a grompp note rather than a warning,
or am I missing something here? This way, there isn't an encouragement
for people to use the -maxwarn option for other situations when it is
On 14/04/17 17:48, Christopher Neale wrote:
> Yup, I use maxwarn all the time in that case. It's safe for general usage.
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Anurag Dobhal <anurag.dobhal at nano-medicine.co.in>
> Sent: 14 April 2017 12:43:18
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Error In Umbrella sampling.
> Dear Gromacs usrs,
> I am running a umbrella sampling simulation between two identical polymer
> chains in water using OPLS AA force field. My system does not have any
> charge. I have successfull generated the different configurations.
> While running the "gmx grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top
> -n index.ndx -o npt0.tpr" command to genetarte the .tpr file I got the
> following warning.
> " You are generating velocities so I am assuming you are equilibrating a
> system. You are using Parrinello-Rahman pressure coupling, but this can
> be unstable for equilibration. If your system crashes, try equilibrating
> first with Berendsen pressure coupling. If you are not equilibrating the
> system, you can probably ignore this warning "
> I am following the Umbrella sampling tutorial by Bevan Lab developed by
> Justin. I have used the npt_umbrella.mdp file given in the tutorial.
> Is is safe to use maxwarn in this case ? or is their any solution to
> overcome this warning ?
> Any help will be highly appreciated. Thank you
> *Anurag Dobhal*
> *Graduate Student (Bioprocess Technology)*
> *Institute of Chemical Technology, Mumbai*
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Dr Thomas Piggot
University of Southampton, UK.
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