Dear all, I run the NPT (anisotropic) for the urea-water system. After the md run the pressure is not closer to 1 bar but in terms of 100. Suggest me the corrections in my parameter file.
-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar Sent: Monday, January 15, 2007 7:54 PM To: Discussion list for GROMACS users Subject: Re: Re: [gmx-users] infinitive force acting on atom during Hi Joern, In any case, you want to first perform an energy minimization in vacuum to release the strain present in your starting structure. Only then can you be sure that if you run into trouble after solvating your system, it is caused by that. It may be that during solvation a solvent molecule is misplaced, but that would more likely cause a "water molecule ... cannot be settled" error. At this point, I would suggest to introduce an additional step of energy minimization prior to solvation. If you still run into trouble then, post again with new details and we can have a more thorough look. > Have you or anyone else got an idea of what goes wrong in my simulation? > And another thing is (perhaps a stupid question ?!?): why is it better > not to use a cubic box for the simulation ? Not a stupid question. For one thing, the cubic box is a waste of resources. The rhombic dodecahedron will give you the same minimum distance between periodic images for 71% of the volume. There's an additional advantage when using a rhombic dodecahedron. Because it corresponds to the densest packing of a sphere, it ensures that you have the same distribution of solvent all around your solute. With a cubic box (or a rectangular box, or a truncated octahedron), you have an uneven distribution and this can potentially affect the results obtained from your simulation. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
minim2.mdp
Description: minim2.mdp
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