Re: SHAKE troubles

From: Arvid Soederhaell <>
Date: Tue 4 Jun 2002 10:22:40 +0200 (MEDT)

Dear Stef, Dac, Yong

Response to Stef and Yong:

>I think it is may be linked to the size of the box. The problem certainly
>occurs because you didn't respect the 'law' which states that to have an
>efficient PME simulation, one needs a cutoff smaller than the distance
>between the solute and the faces of the box : for example 10 Angstroems
for a >9 Angstroems cutoff. >If it works with smaller values, i think the
reason is coming from that point. >Stef

I do not really understand what you mean. The size of the box is about
43x43x77 Angstroms. The lipids in the membrane is of course directly at
the face of the box. (The membrane is an infinite membrane in the X-Y

However, the PME is surely not the problem yet. I do not use PME, while
the anisotropic pressure control and PME does not work together in amber6.
However i'm still intrerested in your point, while i'm going to use PME
when i have got amber7 running. (In amber7 the PME and anisotropic
pressure works together.)

Response to dac

>You don't state whether or not you set the vlimit parameter... > >...dac

Yes, I did, but it crashed anyway!!?? Here is the error message. It is
obviously an explosion as a result from a van der Waals overlap or
something similar. (vlimit=20.0) So the vlimit is exceeded simultaniously
as SHAKE crashes.

 vlimit exceeded for step 24080; vmax = 70.85354277911610

     NITER, NIT, LL, I AND J ARE : 0 0 4608 7491 7493

      A V E R A G E S O V E R 24080 S T E P S


> Thanks for the interest in my SHAKE problems! > > Well, I have still
not succeded to get my membrane-water simulation > running, but it seems
as if i'm not the only one who have had this > problem, as indicated in
the FAQ list (BLOWUP and SHAKE). > > Let me explain the situation in more
detail... > The simulaiton contains lipids, which have strongly charged
headgroups. > (Phosphor has a charge of about +1, surrounded by 4 oxygens
wiht a charge > of about -0.7 each.) The SHAKE problems occur when the
cutoff (CUT) is > increased from 8-9 angstroms to 11-12 angstroms. Before
the increase the > system is prefectly stable (several nanoseconds) using
NVT and NPT > anisotropic thermo/baro-stats. After the increase of cutoff
the system > becomes quite unstable, but it does not blow up immediately.
Sometimes it > runs for 40-50 ps and then crash. This happens in both NVT
and NPT > ensembles. The temperature is set to 323 Kelvin, which suggests
that a > shorter timestep should be used, but no... 1 fs timestep does not
work, > even 0.5 fs makes the system blow up. > > I have tryed to run
minimizations using a long cutoff before restarting > the dynamics, but
this does not improve the situation. > > I believe that it has something
to do wiht the strong charges of the lipid > head groups, but i don't
understand what....
Received on Tue Jun 04 2002 - 01:22:40 PDT
Custom Search