Re: FEP atom velocity.

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Aug 20 2018 - 13:15:01 CDT

Can you tell us which atoms giving the error then? An atom index that high
sounds like a solvent atom and may have nothing to do with FEP. Is your
starting structure and system density well equilibrated?

Cheers,
BKR

On Mon, Aug 20, 2018, 2:12 AM Aashish Bhatt <aashish.ph16221_at_inst.ac.in>
wrote:

> Dear Sir
>
> I want to know free energy of ion with serine nitrogen. I have followed
> Crown ether example in FEP tutorial.
> When i select atoms i got the error below. I am littile bit confusing i
> have not select atom 32438 for free energy calculation.
>
> ERROR: Atom 32438 velocity is -nan -nan -nan (limit is 5000, atom 116 of
> 281 on patch 50 pe 3)
> ERROR: Atom 32439 velocity is -nan -nan -nan (limit is 5000, atom 117 of
> 281 on patch 50 pe 3)
> ERROR: Atom 32440 velocity is nan nan nan (limit is 5000, atom 118 of 281
> on patch 50 pe 3)
> ERROR: Atoms moving too fast; simulation has become unstable (3 atoms on
> patch 50 pe 3).
> ERROR: Exiting prematurely; see error messages above.
>
> Can you suggest me how can performed FEP in a right way.
>
> Regards
>
> Aashish Bhatt
>

This archive was generated by hypermail 2.1.6 : Mon Nov 18 2019 - 23:20:04 CST