Justin,
with cut-offs=1.2 both in cpu+gpu or with cpu only I've obtained only small decrease along the Z-dim ( from 10 to 9 nm). With cut-offs 1.0 I've obtained decreae from 10 to 8.5. So it might be concluded that the observable is cut-off sensetive. By the way during simulation of such system in gromos-54a7 united atom ( the same number of lipids and water) ff with 1.2 cut-offs I didnt observed any decrease of the cutoffs. James 2013/1/29 Justin Lemkul <jalem...@vt.edu>: > > > On 1/29/13 2:19 AM, James Starlight wrote: >> >> 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? >> > > Membranes are very sensitive to cutoff settings. Can you test by running on > CPU only with the normal CHARMM cutoff settings? I would be curious to see > if the shortened cutoffs produce bad results. > > You should not have to make any special changes to the compressibility or > pressure along Z in order for the simulation to be stable. What's happening > to the x and y box vectors? Is the membrane becoming distorted or > compressed? Or is it expanding laterally? > > > >> 2013/1/29 James Starlight <jmsstarli...@gmail.com>: >>> >>> 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 ? >>> > > Certainly you can run in an NVT ensemble if the force field will produce > good results. Normally NPT or NPAT ensembles are most appropriate for > membranes, depending on the parameterization of the lipids. Running in NVT > is as simple as setting "pcoupl = no" while leaving other thermostat-related > items the same. > > -Justin > > >>> >>> James >>> >>> 2013/1/28 Justin Lemkul <jalem...@vt.edu>: >>>> >>>> >>>> >>>> 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 gmx-users@gromacs.org >>>> 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 gmx-users-requ...@gromacs.org. >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > ======================================== > > 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists