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

Mark Abraham Mark.Abraham at anu.edu.au
Mon Nov 14 13:21:45 CET 2011

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.

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