[gmx-users] weird problem on small molecules with triple bonds

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 16 19:27:54 CEST 2007

David Mobley wrote:
> All,
> I may be in a hole of my own digging, here, but I've been trying to
> simulate a large set of small molecules in explicit solvent. I'm using
> the Amber GAFF parameters, converted over to GROMACS using our
> amb2gmx.pl script.
> The problem I'm running into is that for anything with a triple bond
> (i.e. propyne), I get "blowing up", even in vacuum (i.e., I get a
> series of constraints warnings finally ending in a crash). This is
> with a 2 fs timestep. Since of course things with triple bonds have
> larger spring constants, I have tried reducing the timestep, but still
> run into problems with timesteps as small as even 0.5 fs, which is
> ridiculous, especially since the spring constants are not THAT much
> bigger.
> This made me suspect some sort of problem with the conversion script
> with respect to triple bonds, so I went through and hand-checked all
> of the bond, angle, and torsion parameters. Everything appears fine,
> in that manual conversion from the GAFF values gives me the same
> values the script is giving me.
First if you have constraint warnings that means you're not using bonds, 
and hence force constants shouldn't matter.

> I should mention that, if I run these simulations in AMBER, even with
> 2 fs timesteps, I don't have any problems.
> Anyone have any thoughts? I'm a bit at a loss about what else to look at, here.
> One other thing I notice -- which, again, doesn't appear to cause any
> problems in AMBER --  is that GAFF specifies a dihedral force constant
> of zero for the c1-c1-c3-H dihedral in propyne, which means that the
> methyl can rotate rapidly. This doesn't appear to cause any problems
> in AMBER, but I do notice that the LINCS warnings I get relate to
> constraint deviations between c3 and H.
That is a real problem, and I don't know what to do about it execpt 
using SD. How about angles of 180? To do this correctly you might want 
to have C2 above be a virtual site. I assume C1 should be N1.

Otherwise this should not be a problem, so I suspect a topology error.

> Any ideas will be appreciated.
> Thanks,
> David
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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