Hi Michael, are you simulating with a constant area, volume or pressure ensemble? If you are using the configuration you mention as a starting point and simulating it with another forcefield, as Mark pointed out, it's not unexpected to find problems. Moreover, equilibration in lipid simulations... takes time!! At least 10-20 ns of simulation, as a rough estimate. If you are using constant area or volume, observe that a DPPC bilayer has an experimental area per lipid of 64 A**2 at 50 C, so you should start with this value. Regarding constant pressure simulations, your system must reach that value.
Regards. Pedro. 2007/4/6, Mark Abraham <[EMAIL PROTECTED]>:
Michael Skaug wrote: > I am trying to perform a simulation of 128 dppc in 3655 spc water. > I obtained .pdb and .top files from the Biocomputing website at U.Calgary. > I do nothing to alter the structure, which must be minimized as it comes err, not minimized - sampled from the ensemble they were using, which needn't correspond to the ensemble you're using. As soon as you generate new velocities, the source of your structure will only give you the same gross morphology, not an equilibrated system. > from the end of a 1 ns simulation. Processing the input files works fine, > but the mdrun always ends somewhere between step 500 and step 3000. I have > tried adjusting various parameters, such at the time step, tau_p, tau_t and > the compressibility, but nothing has created a consistent run. > I wonder where I should be focusing my time to solve this problem. Should > I focus on the parameters and structure, or computer hardware/software? We can't tell unless you tell us what GROMACS is reporting as the problem. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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