[gmx-users] Error In Umbrella sampling.

[abhisek Mondal]

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>
wrote:

> 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 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
> 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*

*INDIA*