Re: glycam force field with amber

From: David A. Case <>
Date: Fri, 13 Jun 2003 09:42:31 -0700

On Fri, Jun 13, 2003, wrote:
> I'm performing molecular dynamic simulations of an enzyme in presence
> of its substrate. The last one is a sugar (monosaccaride)composed of
> more or less 45 atoms. Owing to the presence of the sugar it is
> necessary to use the glycam force field (2000 version by Woods et al.)
> in addition to the 'normal' amber7 force field (parm99). Performing an
> equilibration dynamic on the solvated enzyme alone (without the sugar
> and without the need of using glycam) requires more or less 30 hours
> for a 50ps long dynamic on a Pentium4 180Mhz machine. When we add the
> sugar (with an increase in size of the system of 45 atoms over more
> than 20000), a dramatic increase of computing time is observed (five
> times). We searched the reason of these increase in the computation of
> hidrogen bonds, but we think these are calculated only between the
> sugar and the surrounding molecules, and not between all the atoms.
> Another explanation could be a problem of compatibility between amber7
> and glycam2000. We would be very pleased to know your opinion about
> this problem and the reasons that could cause it.

There is no reason I can think of why use of the glycam force field would lead
to such a result. You might look at the timing breakdown of the two runs, to
see if the increase in time comes in any particular part of the calculation.
Also, look at the size of the nonbonded list, which should be about the same.
In general, I would suggest that you set the force field issues aside, and
look hard for some other difference between the two runs.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Fri Jun 13 2003 - 17:53:01 PDT
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