[gmx-users] Structure blowing up after increased the temperature

Sameer Edirisinghe nootsam at gmail.com
Wed Mar 22 06:01:08 CET 2017

Thank you for the help Dr. Jsutin

On 3/21/17 12:39 PM, Sameer Edirisinghe wrote:
> Dear users,
> I'm trying to find the melting point and Tg of my polymer system using
> Density vs temperature curve. I'm using all oplsaa forcefield and  I'm
> for NVT and followed by NPT equilibration ( Both at 523K) of 400ps each.
> then after the production run (at 523K for 5ns) the system is blowing up
> and can be observed broken molecules of the trajectory from VMD. But no
> blowing up occurring at 300K temperature (200ns).

"Broken" molecules are a consequence of PBC, not instability.

*I used -pbc nojump flag in trajconv command but still molecules seems to
be broken*

> But if I only did the production run (at 523K) up to 200ps it seems no
> blowing up occurring until 200ps.

Systems simulated at higher temperature will naturally diffuse faster,
cross periodic boundaries more frequently or more quickly.

> Note. used .mdp files has attached with the mail

The mailing list does not accept attachments.

> 1) I'm not sure if the .mdp files caused the blowing up or the topology
> caused the blow up of the system.
> 2) Can use same .mdp files by only changing coupling temperature for any
> temperature?

High-temperature simulations often require shorter time steps and perhaps a
tighter regulation of temperature and pressure to be stable, but as of yet
have no evidence that your simulation was actually unstable.

*Here i used 0.001ps as time step. Do i need to reduce it more ?*

*Pressure and temperature have fluctuations after the equilibration while
pressure seems to have higher fluctuations.*

*see my temperature and pressure coupling options below. I used them for
both equilibrium and production run.*

*tcoupl = Nose-Hoover        *
*tc-grps = MD ; *
*tau_t = 8        ; *
*ref_t = 523          ;*

*; Pressure coupling is on*
*pcoupl        = Parrinello-Rahman     *
*pcoupltype        = isotropic            ; uniform scaling of box vectors*
*tau_p        = 5.0            ; time constant, in ps*
*ref_p        = 1.0            ; reference pressure, in bar*
*compressibility     = 4.46e-5            ; *


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