[gmx-developers] Group cutoff-scheme simulation temperature affected by nh-chain-length

[Du, Yu]

Thanks for Prof. Berk's prompt fix.


You advised that "You should never change the combination rule of a force field" in Bug #2286 and because tabulized potential needs comb-rule=1, what should I do to use the amber99sb-ildn ff? (ff needed for protein-ligand simulation system) Or in Gromacs, I can only use the group cutoff-scheme and tabulized potential with gromos ff?

Could you please explain the consequence I may get when I use the comb-func=1 amber99sb-ildn ff which is changed by myself?


Best, 
Yu

-----Original Messages-----
From:"Du, Yu" <duyu at sioc.ac.cn>
Sent Time:2017-11-02 14:00:40 (Thursday)
To: GMX-developer <gromacs.org_gmx-developers at maillist.sys.kth.se>
Cc:
Subject: Re: [gmx-developers] Group cutoff-scheme simulation temperature affected by nh-chain-length

Dear GMX-Developers and Shirts, 


To reproduce the the problem, I use the material in GROMACS Tutorials Lysozyme in Water.



Yes, Prof. Shirts. If I use standard vdwtype=cut-off, coulombtype=pme and cutoff-scheme=group, the simulation temperature accords with the ref_t.
If I use gromos ff and tabulized  potential, there is no temperature problem.


Now the problem is pinned on the relation between tabulized potential and thermostat under amber99sb-ildn ff.


I filed Bug #2286 in redmine.
https://redmine.gromacs.org/issues/2286


Hope you could give some advice about this issue.


Yu

-----Original Messages-----
From:"Michael R Shirts" <Michael.Shirts at Colorado.EDU>
Sent Time:2017-10-23 19:43:38 (Monday)
To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>, GMX-developer <gromacs.org_gmx-developers at maillist.sys.kth.se>
Cc:
Subject: Re: [gmx-developers] Group cutoff-scheme simulation temperature affected by nh-chain-length



If you can file a bug report in redmine (http://redmine.gromacs.org/) with example files, that would be useful. Before you file it can you check if problem happens if you use standard cutoffs, instead of tabulated cutoffs? I wonder if there is some sort of code path that it’s going down.  I will bet that combination of inputs has only very rarely been used.  Also, you said the temperature jumps. Does it come back down to 310, or does it stay there?

 

Generally, I would recommend using v-rescale instead of Nose-Hoover.  Nose-Hoover has some known flaws; increasing the chain length is supposed to help things, but doesn’t really help that much for realistic systems, just with very simple ones.

 

However, any Nose-Hoover change length should in principle give the same average, and did when the code was written.  If it doesn’t, the code was broken somewhere, possibly because of lack of coverage in the regression tests and something getting out of sync.

 

Best,

~~~~~~~~~~~~~~~~

Michael Shirts

Associate Professor

michael.shirts at colorado.edu

http://www.colorado.edu/lab/shirtsgroup/

Phone: (303) 735-7860

Office: JSCBB C123

Department of Chemical and Biological Engineering

University of Colorado Boulder

 

From: <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> on behalf of "Du, Yu" <duyu at sioc.ac.cn>
Reply-To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
Date: Monday, October 23, 2017 at 12:48 AM
To: GMX-developer <gromacs.org_gmx-developers at maillist.sys.kth.se>
Subject: [gmx-developers] Group cutoff-scheme simulation temperature affected by nh-chain-length

 

Dear GMX Developer and Prof. Hess, 

 

I think this question is not common to GMX users, so I post it here.

 

Prof. Hess is very familiar with the tabulized potential and group cutoff scheme, so I also CC this email to you. Any advice will be appreciated. 

 

The Backgroud:

I simulated protein-ligand system (ref_t=300) with amber99sb-ildn ff. I used the normal table6-12.xvg tabulized potential to reproduce this problem.

 

The Problem:

In NVT simulation, integrator=md-vv, Tcoupl=nose-hoover, coulombtype=pme-user, vdwtype=user. I found that at the start of the simulation, there is a temperature jump to around 310K (average 310K in 100ps) higher than the ref_t (300K) under nh-chain-length=10.

 

1)I tuned and spotted the nh-chain-length parameter. If I used nh-chain-length=1 there is no temperature jump and temperature can converge very well to 300K.

 

2)I replicated the same experiment in verlet scheme, the temperature converged to ref_t 300K in 100ps and no jump in nh-chain-length=2, which can 50K temperature jump (to 350K).

 

The Question:

1)How will the nh-chain-length parameter affect the simulation temperature under the group cut-off scheme?

2)Is it valid to use NH (nh-chain-length=1) not NH chain (nh-chain-length>1) to simulate the protein-ligand system?

 

Thanks for any advice.

 

--

Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry

345 Ling Ling Rd., Shanghai, China. 

Zip: 200032, Tel: (86) 021 5492 5275
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20171102/d74b583c/attachment.html>