One important point: in that simulations I've used decreased cut-offs with charmm36 ff because that systems have been modelled with CPU+GPU so I had some imbalance in cpu\gpu loadings with common (1.2) cutoffs.
rlist = 0.8 ; Cut-off for making neighbor list (short range forces) rlistlong = 1.4 rcoulomb = 0.8 ; long range electrostatic cut-off rvdw = 0.8 Might that affect on the compresbility of my system? Might I prevent such compression by means of changing ref_p or compressibility on the Z using emiisotropic pcoupltype? James 2013/1/29 James Starlight <[email protected]>: > Its intresting that on the same system which was equilibrated longer > the decrease on the Z dim was smaller (from 10 to 9nm). By the way > does it possible to simulate membrane proteins (with explicit > membrane) in the nvt enssemble without explicit barostat ? What > options in the mdp should be added for such simulation ? > > > James > > 2013/1/28 Justin Lemkul <[email protected]>: >> >> >> On 1/28/13 8:45 AM, James Starlight wrote: >>> >>> Justin, >>> >>> yes, 2 A for C atoms. >>> >>> The dims are 8.68740 8.41864 10.00000 >>> >> >> Well, with such a dramatic change, it should be fairly easy to simply watch >> the trajectory and see what went wrong. >> >> >> -Justin >> >> -- >> ======================================== >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
