Re: membrane simulation ERROR rattle algorithm

From: Jorgen Simonsen (
Date: Wed Jul 06 2011 - 03:36:22 CDT

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

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