[gmx-users] Problem about simulation at high temperature and ratio of sencondary stuctures

[Mark Abraham]

On 14/11/2011 8:33 PM, ??? wrote:
>
> Hi Gromacs users,
>
> I am using GROMACS (ver4.5.3) to run molecular dynamics (MD) 
> simulation. However during my simulation runs, I encountered some 
> problems as stated below:
>
> 1. In NPT condition, the box size undergoes changes, especially at 
> high temperature simulations. However, during semisotropic pressure 
> coupling, the box size changed dramatically at x/y or z direction. 
> That made the box thin and long or flat. On the top of that, it caused 
> fatal error in the runs and the simulations stopped running 
> altogether. Can this situation be prevented ? If so, how can it be done?
>

Perhaps the models in your systems are intrinsically unsuited to these 
simulation conditions. To my knowledge, no common biomolecular force 
field has been parametrized against high-temperature NPT data. Under 
these conditions, the assumptions about safe sizes for integration time 
steps need not hold, so you may find smaller steps are more stable.

> 2. I have found that command "g_helix" can calculate helix properties. 
> Nevertheless, my concern is with beta sheet. I did not find any tools 
> in Gromacs that can calculate the ratio of beta sheet from MD 
> trajectories. Do you have any recommendations?
>

do_dssp with old-style DSSP installed is the only GROMACS offering that 
can address this. Check out manual section 7.4 for overviews of tools.

Mark
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