Re: Stray PME grid charges detected

From: Sourav Ray (
Date: Mon Apr 04 2016 - 13:12:41 CDT

I would suggest you to do sequential relaxation, first say keep the main
chain backbone atoms and side chain backbone atoms fixed and then only keep
the main chain backbone atoms fixed, you may find the gramicidin tutorial
useful though.

On Mon, Apr 4, 2016 at 11:32 PM, faride badalkhani <> wrote:

> Hi,
> Thank you for the useful comments. I made the changes you said and started
> a new simulation, and I am waiting for the result. However, I have a
> question! Is that possible this error caused by the starting configuration?
> Because it is a hyperbranched polymer.
> Regards,
> Farideh
> On Mon, Apr 4, 2016 at 6:26 AM, Sourav Ray <>
> wrote:
>> Hello
>> 1. I think the timestep is too small (0.1 fs, usually 1 fs is minimum
>> that is employed). Please confirm from previous literature.
>> 2. Use a higher langevin damping constant for the thermostat, like say
>> 10/ps, it solves a lot of issues during equilibration/relaxation.
>> 3. If constant pressure is not working, either increase the margin from
>> default 0 to say 5 or turn the flexible cell and constant area option on--089e01537b62b21df7052facac05--

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