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

Du, Yu duyu at sioc.ac.cn
Mon Oct 23 08:49:01 CEST 2017

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
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