Re: membrane simulation ERROR rattle algorithm

From: Salvatore Mario Cosseddu (
Date: Wed Jul 06 2011 - 06:15:46 CDT



if you choose 2 fs and rigid all, according to the manual you can use
only values less then

fullElectFrequency 3
nonbondedFreq 1

Did you change some of those parameters?

Once I did, just to see the effect, and the result was similar to what
you are describing.


On 06/07/11 09:36, Jorgen Simonsen wrote:
> Thanks - so the atoms do not look strange - nor on top of each other.
> I tried to change the integration step to 1 fs from 2 fs and the
> simulation could run (without any minimization just to test) - I let
> the simulation run for a 5 - 10 ps and then I restart the simulation
> with a 2 fs integration step and it fails again same error message but
> different atom.
> If I run the whole system without any constraints on headgroups,
> water, or protein it is not a problem and I can run with 2 fs - I find
> this a little bit strange
> Should I run longer(more minimization?) or should other things be test
> before this?
> On Tue, Jul 5, 2011 at 8:40 PM, Ajasja Ljubetič
> <> wrote:
>>> BTW: a tip for lazy people:
>>> use "serial" instead of "index" in the selection string
>>> and you don't need to decrease by one. ;)
>> Oh, good one! wish I knew this before I wrote a couple of (now useless) tcl
>> VMD_to_NAMD_index and NAMD_to_VMD_index routines :)
>> Best regards,
>> Ajasja

Salvatore Cosseddu
PhD student
Centre for Scientific Computing and School of Engineering
University of Warwick
Coventry CV4 7AL
United Kingdom

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