Dear Ross,
I am attaching the input files I have used for the simulation. What I do
is the following: I do a restraint run for 30ps during which I increse the
temperature (files 2pel.0000_0010.in, 2pel.0010_0020.in and
2pel.0020_0030.in). And after that I run the simulation without any
restrain on the protein.
My boundary conditions are correct: NTB=2 and NTP=1 and during increase of
temrature NTB=1. And my cutoff is 10 angstroms, not 8 angstroms. Is that a
high value ? Also, by box size I mean that during solvation I put buffer
of 8 angstroms from the farthest atom of the protein and so as you said my
box size is 16A + the diameter of the protein.
Also I am measuring the RMSD of only the protein. RMSD of the same protein
for a simulation of 2ns at 300K is about 2 angstrom. So I thought at 600K
RMSD value of 8 angstrom is okay. Is such high RMSD not correct ?
Thanks for your reply and I hope to get some more clarifications.
-Priti
> Dear Priti,
>
> Unless there is something wrong with your simulation you should never need
> to change the value of lastrst. There is a reason it does not appear in
> the
> manual.
>
> There is also no relationship between lastrst and taup. The first controls
> memory allocation while the second controls the barostat relaxation time.
> Unless you have a specific reason for wanting to change the pressure
> relaxation I would leave taup at the default value. Instability in the
> trajectory often comes from other places 'before' it comes from the
> pressure
> coupling.
>
> It would be useful to see your input files and the protocols you used. If
> you hot started at such a high temperature you are almost certainly likely
> to have an unstable system. At 600 K you may also need to reduce the
> timestep from say 2fs (with shake) to 1.5fs or so.
>
> Also, are your boundary conditions correct? NTB=2 and NTP=1?
>
> You also note that the calculation of pressure is very inaccurate at low
> temperatures and so the barostat can over correct leading to instability.
> You should always start your heating from 0K with constant volume (NTB=1)
> and then after say 20ps or so when you are above 100K you can switch to
> constant pressure (NTB=2).
>
> It would also be useful to see what you set the cutoff value to. Typically
> lastrst errors come from setting a massive cutoff. If you are running a
> periodic boundary simulation with PME then you only need a cutoff of 8
> angstroms.
>
> I am also not sure what you mean by box size of 8A - this seems incredibly
> small. Do you mean this is the buffer size you used in Leap when solvating
> the system? If this the case then your box size will be 16A + the diameter
> of your molecule in X Y and Z directions. You can check the output file
> where the box size should be printed.
>
> With regards to the RMSD both values seem very high and suggest a problem
> with the trajectory. This assumes of course that you are measuring the
> RMSD
> of the protein and not of the whole system. Since water molecules are not
> reimaged during a PME simulation your RMSD will just keep increasing as
> you
> run a simulation. Hence the rmsd you are interested in is the solute RMSD.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
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Received on Sun Oct 29 2006 - 06:07:14 PST
