Dear Justin, Indeed I didnt take into account square degree so all values presented in the tutorial exactly true so this was exactly my mistake. :(
After some iterations I've obtained value for S per lipid beetween 0.65-0.71 A^2. This is the example of the system wich I've obtained after solvation and futher minimization. http://www.sendspace.com/file/h6urhq It looks good. :) By the way I'd like to know about correct value for the S per protein ? Where I can obtain such information for my protein ? ( e.g for big proteins such receptors and channels ) The error with GenBox was due to the big vdv R for the carbons. It's intresting that I couldnt increase this value mush as 1.2. But my finally system didnt consist of some water within the membrane so I supose that it's good. Now my system on the stage of the equilibtation so I have not any questions yet but I only wounder to know about teqnique of the force fied preparation for the membrane protein simulation. In this work I've done this step in accordance with the tutorial. On the last stage I've copied gromos53a6_lipid.ff directory in $GMXLIB so now I can use it in pdb2gmx for instance. But when I've tried to make gro and top files for my lipid.pdb via pdb2gmx I've obtained errors that Residue 'DPP' not found in residue topology database so I think that in addition to the operations wich I've already done I should also make some changes in the /gromos53a6_lipid.ff/aminoacids.hdb ./gromos53a6_lipid.ff/aminoacids.n.tdb ./gromos53a6_lipid.ff/aminoacids.c.tdb shouldn't I? Finally, I've heard that there are already pre-build force fields for the membrane smulation. E.g I've heard that there is some modified CHARMM ff wich gave good results in simulation. Do you know something about this? Thank you for your help, James
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