[gmx-users] Gromacs versions 4.0.5 and 4.5.4

Itamar Kass itamar.kass at monash.edu
Thu Oct 20 00:17:03 CEST 2011

Hi Sopna,

First, can you attached the crash report of GROMACS 4.5, so we can have a look on it? Second, are you doing EM and PR before you run it using 4.5? Even if you transfer a stable system from 4.0 it might need some equilibration before you actually run MD, specifically if you assign new velocities to atoms.


On 20/10/2011, at 8:40 AM, Sapna Sarupria wrote:

> Hello,
> I did change nsttcouple and nstpcouple but the simulations that run in 4.0.5 are still crashing in 4.5.4. I think it is related to constraints but I am unable to figure out exactly what is different. I have pasted both my topology and mdp (updated for 4.5.4) files. Any ideas? I have read through the manual and it seems like the mdp files does not need any changes, but perhaps I am missing something.
> Thank you for your help!
> Sincerely,
> Sapna

> nstxout           =  0000                    ; write coords

What that mean? You better give a number bigger than 0.

> gen_seed             =  372340                   ; random seed

Just a remark, you can use -1 here for a random number base on time and process number.

> constraint_algorithm = shake

Any reason why not to using LINCS?

"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut

| Itamar Kass, Ph.D.
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