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

[David van der Spoel]

David Mobley wrote:
> David,
> 
> On 10/16/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>> 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.
> 
> Constraints is "h-bonds".
OK.

> 
>>> 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.
> 
> "SD"? Stochastic dynamics? Incidentally, that IS what I'm using, but
> it's not clear to me how it would help.
The problem you could get ith free rotation is build-up of rotational 
energy without barrier to stop it, in particular with Berendsen 
coupling. SD would prevent that.

> 
> And I'm sorry, what do you mean C2 and N1? There are no nitrogens in
> the compound -- it's just propyne. And how would a virtual site help?
> I'm just confused about what you're getting at here -- maybe could you
> give me a tiny bit more detail?
Sorry, my brain was on vacation (about the N). Anyway, having C2 as VS 
would mean the molecule remains perfectly linear as it should be, and 
you do not have to define angles of 180 degrees which gives you an 
ill-defined force.

> 
>> Otherwise this should not be a problem, so I suspect a topology error.
> 
> I thought that too but haven't been able to find one, and as I noted
> these are created by a script.
> 
> Thanks,
> David
> 
> 
>>> 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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-- 
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