[gmx-users] Polymer Relaxation Issue

[Justin Lemkul]

On 1/13/14, 5:21 PM, decaiyu wrote:
> Dear All,
>
> I created a polymer topology with Gromos43a1.ff force field.
> I am running simulation to try to validate my force field.
> When I run a NVT (300K) simulation for 500 ps for a 50-unit polymer without
> periodic boundary conditions, it seems that the polymer just vibrates
> without signifcant relaxation from its initial configuration.
> But when I do the same NVT simulation for the same polymer structure with
> COMPASS force field with Materials Studio, the polymer quickly relaxes (from
> a linear polymer into a coiled structure).
>
> What could be the issue here? The dihedral potential and the bond angle
> potential too strong, or the vDW potential attraction is not strong enough?
>

It sounds like you have some sort of restraints applied during the simulation, 
but without a complete .mdp file, there's no way to tell.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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