[gmx-users] Error In Umbrella sampling.

Christopher Neale chris.neale at alum.utoronto.ca
Fri Apr 14 18:48:16 CEST 2017

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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