[gmx-users] Flat-bottomed potential from user-defined reference

[Cosseddu, S.M.]

Thanks Vitaly,

However, the manual actually say something slightly different, that is "These [restraints] are used to restrain particles to fixed reference positions Ri". From a quick look to the sources this is something that depends on pos0A and (in certain cases) on  a lambda and pos0B. Please, correct me if I am wrong.

>From a theoretical point of view the function that computes such restraints should be happy with  any reference. With user-defined reference, equilibration of the system might be more difficult, and worst case scenario everything blows up because of the excessively-strong forces, but these are a user issues.   

My question is: is there any ways to set pos0A to some user-defined value? If this is not possible, it is because of the parallellisation scheme, and what is the most suitable method to implement such a spherical flat-bottomed potential?  

I tried providing grompp with a structure file containing my user-defined pos0A via -c (i.e. coords of the relevant atoms were set to the center of my sphere), while my initial configuration and velocities were provided via -t and a cpt. Unfortunately it  didn't work.   

Many thanks
Salvatore

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Vitaly V. Chaban [vvchaban at gmail.com]
Sent: 03 November 2015 11:47
To: gmx-users
Subject: [Spam] Re: [gmx-users] Flat-bottomed potential from user-defined reference

Gromacs uses restraints to keep molecules near their original positions.
See the manual.




On Tue, Nov 3, 2015 at 8:24 AM, Cosseddu, S.M. <s.m.cosseddu at vu.nl> wrote:

> Dear all,
>
> I am trying to apply a spherical flat-bottomed potential to maintain some
> molecules within a certain region. By default, GROMACS uses the initial
> coordinates as reference. Is there any way to provide different references?
>
> Many thanks
> Salvatore
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