[gmx-users] Error In Umbrella sampling.
mark.j.abraham at gmail.com
Tue May 9 09:21:15 CEST 2017
It'd safe for general usage if your volume is already approximately
correct. But it has been a frequent occurrence here that people follow
tutorial methodology outside of that context, and use such coupling when
that condition is not true, leading to failed simulations. We aim grompp
warnings to cover cases of "this may be a bad idea" but let the user assert
that they know what they are doing. We hope that overall this improves the
impression of usability, but that is hard to judge!
On Mon, 8 May 2017 18:30 abhisek Mondal <abhisek.mndl at gmail.com> wrote:
> Every time I ran through this step I needed to use -maxwarn. It raises no
> issues later on.
> On Fri, Apr 14, 2017 at 11:42 PM, Thomas Piggot <t.piggot at soton.ac.uk>
> > 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 less
> > appropriate.
> > Cheers
> > Tom
> > On 14/04/17 17:48, Christopher Neale wrote:
> >> Yup, I use maxwarn all the time in that case. It's safe for general
> >> ________________________________________
> >> 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
> >> 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
> >> 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
> > Visiting Fellow
> > University of Southampton, UK.
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> Abhisek Mondal
> *Senior Research Fellow*
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
> *Kolkata 700032*
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