Dear users, Trying to perform a MD for a peptide 12aa long.
Following the tutorial for peptides MD: http://www.gromacs.org/documentation/reference/online/speptide.html everything seems fine till I reach PR MD. First I get a warning for grompp: WARNING 1 [file aminoacids.dat, line 1]: T-Coupling group Protein has fewer than 10% of the atoms (201 out of 5150) Maybe you want to try Protein and Non-Protein instead? WARNING 2 [file aminoacids.dat, line 1]: T-Coupling group K+ has fewer than 10% of the atoms (5 out of 5150) Maybe you want to try Protein and Non-Protein instead? I thought, I need to change tc-grps = Protein SOL K+ ; Time constant (ps) and reference temperature (K) = tau-t = 0.1 0.1 0.1 ref-t = 300 300 300 TO ; Groups to couple separately = tc-grps = Protein Non-protein ; Time constant (ps) and reference temperature (K) = tau-t = 0.1 0.1 ref-t = 300 300 but, when trying to run grompp again 01 warning is still there (once it is related to the protein group). Not really sure if using non-protein for the sol and ion is really helping (!!??) WARNING 1 [file aminoacids.dat, line 1]: T-Coupling group Protein has fewer than 10% of the atoms (201 out of 5150) I downloaded all the files for the tutorial exercise (speptide - a 19aa long) and I get the same problem. However this warning seems not to be too important, since there is no mention to it at the tutorial. The main difference between my system and the tutorial one is the non-charge zero for the system. For that I have added 5 K+ to it. But, of course, for the tutorial I run step by step with no alteration. But, when running MD: mdrun -v pr.mdp -s topol.tpr Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 1 and 2) rms inf bonds that rotated more than 30 degrees: and MD crashes. And again I get this error for my system and for speptide (the tutorial exercise). I am using gromacs 3.3 and have tried 0: GROMOS96 43a1 force field and 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) I am wondering why I am having so much trouble, even when running the tutorial. Any help would be much appreciated. Thanks in advance, Luciane Dr Luciane Vieira de Mello School of Biological Sciences Room 2.20, Life Science Building Tel:(+44) 151 795 5140 FAX:(+44) 151 794 5130 University of Liverpool Crown St.,Liverpool L69 7ZB, U.K.
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