[gmx-users] lipid relaxation time
Dear All, I have a question regarding relaxation time for lipids in simulation. I will be thankful if anyone can help me with this. Actually I want to find the relaxation time so that I can estimate the required time for equilibration before starting production MD. Does anyone know which parameter should be considered as a sign of enough equilibration. I mean when we can say the lipid is relaxed and it is in equilibration? Thanks in advance. Neda -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] [Spam-FG] [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation
Dear Mark, I removed different residues from my energy group list, but still the problem of very large negative pressure exist. Any other solution? Thanks in advance. Neda - Original Message - From: Neda Rafiee To: gmx-us...@gromacs.org Sent: Mon, 16 Jul 2018 12:03:34 +0430 (IRDT) Subject: Re: [gmx-users][Spam-FG] [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation Dear Mark, Thanks a lot for your useful suggestions Neda - Original Message - From: Mark Abraham To: gmx-us...@gromacs.org Sent: Mon, 16 Jul 2018 11:49:38 +0430 (IRDT) Subject: Re: [gmx-users] [Spam-FG] [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation Hi, I presume that's because you still have interactions between groups that are frozen. You can make your life easier by using only the groups you need for your simulation, e.g. those needing a table and those that are frozen. If you are trying to get per-residue decomposition, then (first) make sure your force field was parametrized such that this is meaningful (most aren't), and prefer to do that analysis using mdrun -rerun. mdrun goes slower for each energy group that has interactions to compute, so minimize that. I would also have done a simulation with just my slab and found this pressure issue back then. It is good practice to add complexity to models incrementally, after validating your expectations on the simulation at the previous stage. Mark On Mon, Jul 16, 2018 at 9:07 AM Neda Rafiee wrote: > Dear Justin, > I added the following energy exclusion pairs to my mdp file. Now potential > energy decreased significantly but still I have a very large negative > pressure (minus 10 to power 28) in my system. It seems that pressure is the > same as before.Should I do anything else? > > energygrp-excl= SIB SIB SIB OXB SIB OMB SIB SiSil SIB OSil SIB SiGem > SIB OGem OXB OXB OXB OMB OXB SiSil OXB OSil OXB SiGem OXB OGem OMB > OMB OMB SiSil OMB OSil OMB SiGem OMB OGem SiSil SiSil SiSil OSil > SiSil SiGem SiSil OGem OSil OSil OSil SiGem OSil OGem SiGem SiGem > SiGem OGem OGem OGem > > Thanks > Neda > > - Original Message - > From: Neda Rafiee > To: gmx-us...@gromacs.org > Sent: Mon, 16 Jul 2018 00:01:35 +0430 (IRDT) > Subject: [Spam-FG][gmx-users] > [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation > > http://nospammer.net/SubmitSpam/submitspam.php?id=I3RWR3EnBQVzelBffkN1 > > VA__=e3gwAc6BBLhoIzFgaiVlc3l4NCx2MTOLAFdFHFAKSh8WC0RNG1xWBkZNVBhFdhATFBF > > AfwZQXlsbVlMBA1EWARgVGlweQQwdDB54XzhyJB08IHZEPFVrMhBFVwckFGh7IR9rc1BCWhNVRgI > <http://nospammer.net/SubmitSpam/submitspam.php?id=I3RWR3EnBQVzelBffkN1VA__=e3gwAc6BBLhoIzFgaiVlc3l4NCx2MTOLAFdFHFAKSh8WC0RNG1xWBkZNVBhFdhATFBFAfwZQXlsbVlMBA1EWARgVGlweQQwdDB54XzhyJB08IHZEPFVrMhBFVwckFGh7IR9rc1BCWhNVRgI> > > LWEQ2RCwUXkgZeEkyBUJYOgZGVh1NNndURHxnOl9iWiYOZjQVNj12HEN1WDUrZgA6LUEiFhM1BlQ > > He2QiEEZpC2cvDSIBDH5kEXRRJgNuVycBbD05ESluekcIaiwDZmUNKWgdExQXWHYudwYRLHFAJAF > > zLTM*MXlkEXh1IgB2YCooczcpFRBSehFzexctcjxmJWdVBisxU0csZmI5LnF3KTBkMxU6MHVYP2J > > EdGgjM2xqJWVxeXg7RhddVhkDVl0sHFFLFB0NNCx2MzN0aCMxbGowAhwBVUFfE0NANA9RXgELRhZ > > fFgpTLHYxMXRoIzFsaiWaGQ0MRBZZHl0bG1NQAQdAF18XHUADJURRGQFXYhwLSEoCDBpZRQJCQxU > > FDUEEGhoMFUQxB34hcGEbH0ZpNSthDhkfHl9iRzw5Iyl8bkoZTAJMHEtTHVxFeUVZG0EDI18jGhg > > RYkAVAl9AJmBJXidxKAA4PlBqPndyPztLRjUsTiM*PhANeTRWVzs9Ygk2KVIKNTEUUCF8YGIMPmZ > pBC9iM0A4IXUcGX1rHAdtYwBecT1BHRp8ejRkex8MYHQuDUEtIw06cUczVHQMAHtmLSdgMxoKIn > > B.IGh3DABGaToBazAaKHU.ajRaRDwpW3AiPXQgEy8sehwXcnYMCmReADB9ZXF5ejQsdjEzdGh9WR > > geVV9eVhVVQgNQX1oPUV4BC0YWXxYKUwMSXlABBUZfGAtRDB4XV1dZBENWGhwMRB8PV0gWDBFQSV > > lcVwRFTEEYA0oLAlcQQEEaEl0bBg5UHR9MCRgbCl1ZGxxeEGgjMW5qJWVweXg0Nx5FRwRSDB4bHV > > JLBREdWEkbWkYYBEJTQglKCHF5eDYsdjEzdGgjCgQeURVLVldDWwEfVAYHTlAPGQsKAx5XZ1kGQV > > wGHAx8DQNJDB8eJ3hFBUVAWy9uaUE*VgADCid4RQVFM3RoITFsaiVlcXlUXFgCQQlbR1RGG0RCFx > > 4UGVdfWF5BE0dwRBwaShcFVjVVRRpYXRM3b1gfHlZlcXl6NCx2MTN0aGFZGB5VFktWV1lNH11fHR > > tXHx8TVksaDRAaXxMeXhUBT1wNBAoJGAoMXUIQXhwTGkxcDQlWSx4LH2tLG0keARtGQx9qJWVzeX > > g0LHYxM2kPTklBH1YAAwpVRkkHRFYHHGNWHgVIBBIKVlteETEzdGwjMWxqJWVxYXg0LHcxM3v0yu > ILmFi9OA8Sb.IVubYVMyMxbG4lZXF5eDQsbjEzdGojMW0HyGY2m9p1eztByEYRoCDQ3g__" > target="_blank"> > If this email is not spam, click here to submit the signatures to > FortiGuard - AntiSpam Service. > > http://nospammer.net/SubmitSpam/submitspam.php?id=I3RWAlEXBhJdXFxffkN1 > > Xg__=e3g2aS5UljdoIzFmaiVlc3l4NCx2MTN7AkJdCQdOEB05DkACE1VGdGgjM2xqJWVxeXg > > hSxtJHgEbRkMfKkIXHhQZV19YXkETaCMxbmolZXF5eDRqHkVHBFIMHgIFVhUQFBVRXlhfVgBHcEQ > <http://nospammer.net/SubmitSpam/submitspam.php?id=I3RWAlEXBhJdXFxffkN1Xg__=e3g2aS5UljdoIzFmaiVlc3l4NCx2MTN7AkJdCQdOEB05DkACE1VGdGgjM2xqJWVxeXghS
Re: [gmx-users] [Spam-FG] [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation
Dear Mark, Thanks a lot for your useful suggestions Neda - Original Message - From: Mark Abraham To: gmx-us...@gromacs.org Sent: Mon, 16 Jul 2018 11:49:38 +0430 (IRDT) Subject: Re: [gmx-users] [Spam-FG] [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation Hi, I presume that's because you still have interactions between groups that are frozen. You can make your life easier by using only the groups you need for your simulation, e.g. those needing a table and those that are frozen. If you are trying to get per-residue decomposition, then (first) make sure your force field was parametrized such that this is meaningful (most aren't), and prefer to do that analysis using mdrun -rerun. mdrun goes slower for each energy group that has interactions to compute, so minimize that. I would also have done a simulation with just my slab and found this pressure issue back then. It is good practice to add complexity to models incrementally, after validating your expectations on the simulation at the previous stage. Mark On Mon, Jul 16, 2018 at 9:07 AM Neda Rafiee wrote: > Dear Justin, > I added the following energy exclusion pairs to my mdp file. Now potential > energy decreased significantly but still I have a very large negative > pressure (minus 10 to power 28) in my system. It seems that pressure is the > same as before.Should I do anything else? > > energygrp-excl= SIB SIB SIB OXB SIB OMB SIB SiSil SIB OSil SIB SiGem > SIB OGem OXB OXB OXB OMB OXB SiSil OXB OSil OXB SiGem OXB OGem OMB > OMB OMB SiSil OMB OSil OMB SiGem OMB OGem SiSil SiSil SiSil OSil > SiSil SiGem SiSil OGem OSil OSil OSil SiGem OSil OGem SiGem SiGem > SiGem OGem OGem OGem > > Thanks > Neda > > - Original Message - > From: Neda Rafiee > To: gmx-us...@gromacs.org > Sent: Mon, 16 Jul 2018 00:01:35 +0430 (IRDT) > Subject: [Spam-FG][gmx-users] > [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation > > http://nospammer.net/SubmitSpam/submitspam.php?id=I3RWR3EnBQVzelBffkN1 > > VA__=e3gwAc6BBLhoIzFgaiVlc3l4NCx2MTOLAFdFHFAKSh8WC0RNG1xWBkZNVBhFdhATFBF > > AfwZQXlsbVlMBA1EWARgVGlweQQwdDB54XzhyJB08IHZEPFVrMhBFVwckFGh7IR9rc1BCWhNVRgI > <http://nospammer.net/SubmitSpam/submitspam.php?id=I3RWR3EnBQVzelBffkN1VA__=e3gwAc6BBLhoIzFgaiVlc3l4NCx2MTOLAFdFHFAKSh8WC0RNG1xWBkZNVBhFdhATFBFAfwZQXlsbVlMBA1EWARgVGlweQQwdDB54XzhyJB08IHZEPFVrMhBFVwckFGh7IR9rc1BCWhNVRgI> > > LWEQ2RCwUXkgZeEkyBUJYOgZGVh1NNndURHxnOl9iWiYOZjQVNj12HEN1WDUrZgA6LUEiFhM1BlQ > > He2QiEEZpC2cvDSIBDH5kEXRRJgNuVycBbD05ESluekcIaiwDZmUNKWgdExQXWHYudwYRLHFAJAF > > zLTM*MXlkEXh1IgB2YCooczcpFRBSehFzexctcjxmJWdVBisxU0csZmI5LnF3KTBkMxU6MHVYP2J > > EdGgjM2xqJWVxeXg7RhddVhkDVl0sHFFLFB0NNCx2MzN0aCMxbGowAhwBVUFfE0NANA9RXgELRhZ > > fFgpTLHYxMXRoIzFsaiWaGQ0MRBZZHl0bG1NQAQdAF18XHUADJURRGQFXYhwLSEoCDBpZRQJCQxU > > FDUEEGhoMFUQxB34hcGEbH0ZpNSthDhkfHl9iRzw5Iyl8bkoZTAJMHEtTHVxFeUVZG0EDI18jGhg > > RYkAVAl9AJmBJXidxKAA4PlBqPndyPztLRjUsTiM*PhANeTRWVzs9Ygk2KVIKNTEUUCF8YGIMPmZ > pBC9iM0A4IXUcGX1rHAdtYwBecT1BHRp8ejRkex8MYHQuDUEtIw06cUczVHQMAHtmLSdgMxoKIn > > B.IGh3DABGaToBazAaKHU.ajRaRDwpW3AiPXQgEy8sehwXcnYMCmReADB9ZXF5ejQsdjEzdGh9WR > > geVV9eVhVVQgNQX1oPUV4BC0YWXxYKUwMSXlABBUZfGAtRDB4XV1dZBENWGhwMRB8PV0gWDBFQSV > > lcVwRFTEEYA0oLAlcQQEEaEl0bBg5UHR9MCRgbCl1ZGxxeEGgjMW5qJWVweXg0Nx5FRwRSDB4bHV > > JLBREdWEkbWkYYBEJTQglKCHF5eDYsdjEzdGgjCgQeURVLVldDWwEfVAYHTlAPGQsKAx5XZ1kGQV > > wGHAx8DQNJDB8eJ3hFBUVAWy9uaUE*VgADCid4RQVFM3RoITFsaiVlcXlUXFgCQQlbR1RGG0RCFx > > 4UGVdfWF5BE0dwRBwaShcFVjVVRRpYXRM3b1gfHlZlcXl6NCx2MTN0aGFZGB5VFktWV1lNH11fHR > > tXHx8TVksaDRAaXxMeXhUBT1wNBAoJGAoMXUIQXhwTGkxcDQlWSx4LH2tLG0keARtGQx9qJWVzeX > > g0LHYxM2kPTklBH1YAAwpVRkkHRFYHHGNWHgVIBBIKVlteETEzdGwjMWxqJWVxYXg0LHcxM3v0yu > ILmFi9OA8Sb.IVubYVMyMxbG4lZXF5eDQsbjEzdGojMW0HyGY2m9p1eztByEYRoCDQ3g__" > target="_blank"> > If this email is not spam, click here to submit the signatures to > FortiGuard - AntiSpam Service. > > http://nospammer.net/SubmitSpam/submitspam.php?id=I3RWAlEXBhJdXFxffkN1 > > Xg__=e3g2aS5UljdoIzFmaiVlc3l4NCx2MTN7AkJdCQdOEB05DkACE1VGdGgjM2xqJWVxeXg > > hSxtJHgEbRkMfKkIXHhQZV19YXkETaCMxbmolZXF5eDRqHkVHBFIMHgIFVhUQFBVRXlhfVgBHcEQ > <http://nospammer.net/SubmitSpam/submitspam.php?id=I3RWAlEXBhJdXFxffkN1Xg__=e3g2aS5UljdoIzFmaiVlc3l4NCx2MTN7AkJdCQdOEB05DkACE1VGdGgjM2xqJWVxeXghSxtJHgEbRkMfKkIXHhQZV19YXkETaCMxbmolZXF5eDRqHkVHBFIMHgIFVhUQFBVRXlhfVgBHcEQ> > > OB0wRIgkZWQMFRFEZAVdCHAtISwERCAtFEgx6Rzp0cD4FUgApIDlwRx5XVR8mEjFsaidlcXl4NCx > > 2b1sAHFMLQ0VIBB8MGVgCEUNcGQlAQkIFVwJeHRdXWRtUXQAJV1gDBAoGBAsKUUICHkYHDVEcCx9 > > MARRWFVBcW15DAAFMXx9ETREcFVtaQxgcVgUdSl0FCFcMBBRVWUh2MTN2aCMxbWolZWoRDEBcTB4 > > cAx9UHxgCQAkUFBNBQBpQUVoLTFxsaiVncXl4NCx2MQgcHFdBVkUKEg
Re: [gmx-users] [Spam-FG] [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation
Dear Justin, I added the following energy exclusion pairs to my mdp file. Now potential energy decreased significantly but still I have a very large negative pressure (minus 10 to power 28) in my system. It seems that pressure is the same as before.Should I do anything else? energygrp-excl= SIB SIB SIB OXB SIB OMB SIB SiSil SIB OSil SIB SiGem SIB OGem OXB OXB OXB OMB OXB SiSil OXB OSil OXB SiGem OXB OGem OMB OMB OMB SiSil OMB OSil OMB SiGem OMB OGem SiSil SiSil SiSil OSil SiSil SiGem SiSil OGem OSil OSil OSil SiGem OSil OGem SiGem SiGem SiGem OGem OGem OGem Thanks Neda - Original Message - From: Neda Rafiee To: gmx-us...@gromacs.org Sent: Mon, 16 Jul 2018 00:01:35 +0430 (IRDT) Subject: [Spam-FG][gmx-users] [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation http://nospammer.net/SubmitSpam/submitspam.php?id=I3RWR3EnBQVzelBffkN1 VA__=e3gwAc6BBLhoIzFgaiVlc3l4NCx2MTOLAFdFHFAKSh8WC0RNG1xWBkZNVBhFdhATFBF AfwZQXlsbVlMBA1EWARgVGlweQQwdDB54XzhyJB08IHZEPFVrMhBFVwckFGh7IR9rc1BCWhNVRgI LWEQ2RCwUXkgZeEkyBUJYOgZGVh1NNndURHxnOl9iWiYOZjQVNj12HEN1WDUrZgA6LUEiFhM1BlQ He2QiEEZpC2cvDSIBDH5kEXRRJgNuVycBbD05ESluekcIaiwDZmUNKWgdExQXWHYudwYRLHFAJAF zLTM*MXlkEXh1IgB2YCooczcpFRBSehFzexctcjxmJWdVBisxU0csZmI5LnF3KTBkMxU6MHVYP2J EdGgjM2xqJWVxeXg7RhddVhkDVl0sHFFLFB0NNCx2MzN0aCMxbGowAhwBVUFfE0NANA9RXgELRhZ fFgpTLHYxMXRoIzFsaiWaGQ0MRBZZHl0bG1NQAQdAF18XHUADJURRGQFXYhwLSEoCDBpZRQJCQxU FDUEEGhoMFUQxB34hcGEbH0ZpNSthDhkfHl9iRzw5Iyl8bkoZTAJMHEtTHVxFeUVZG0EDI18jGhg RYkAVAl9AJmBJXidxKAA4PlBqPndyPztLRjUsTiM*PhANeTRWVzs9Ygk2KVIKNTEUUCF8YGIMPmZ pBC9iM0A4IXUcGX1rHAdtYwBecT1BHRp8ejRkex8MYHQuDUEtIw06cUczVHQMAHtmLSdgMxoKIn B.IGh3DABGaToBazAaKHU.ajRaRDwpW3AiPXQgEy8sehwXcnYMCmReADB9ZXF5ejQsdjEzdGh9WR geVV9eVhVVQgNQX1oPUV4BC0YWXxYKUwMSXlABBUZfGAtRDB4XV1dZBENWGhwMRB8PV0gWDBFQSV lcVwRFTEEYA0oLAlcQQEEaEl0bBg5UHR9MCRgbCl1ZGxxeEGgjMW5qJWVweXg0Nx5FRwRSDB4bHV JLBREdWEkbWkYYBEJTQglKCHF5eDYsdjEzdGgjCgQeURVLVldDWwEfVAYHTlAPGQsKAx5XZ1kGQV wGHAx8DQNJDB8eJ3hFBUVAWy9uaUE*VgADCid4RQVFM3RoITFsaiVlcXlUXFgCQQlbR1RGG0RCFx 4UGVdfWF5BE0dwRBwaShcFVjVVRRpYXRM3b1gfHlZlcXl6NCx2MTN0aGFZGB5VFktWV1lNH11fHR tXHx8TVksaDRAaXxMeXhUBT1wNBAoJGAoMXUIQXhwTGkxcDQlWSx4LH2tLG0keARtGQx9qJWVzeX g0LHYxM2kPTklBH1YAAwpVRkkHRFYHHGNWHgVIBBIKVlteETEzdGwjMWxqJWVxYXg0LHcxM3v0yu ILmFi9OA8Sb.IVubYVMyMxbG4lZXF5eDQsbjEzdGojMW0HyGY2m9p1eztByEYRoCDQ3g__" target="_blank"> If this email is not spam, click here to submit the signatures to FortiGuard - AntiSpam Service. http://nospammer.net/SubmitSpam/submitspam.php?id=I3RWAlEXBhJdXFxffkN1 Xg__=e3g2aS5UljdoIzFmaiVlc3l4NCx2MTN7AkJdCQdOEB05DkACE1VGdGgjM2xqJWVxeXg hSxtJHgEbRkMfKkIXHhQZV19YXkETaCMxbmolZXF5eDRqHkVHBFIMHgIFVhUQFBVRXlhfVgBHcEQ OB0wRIgkZWQMFRFEZAVdCHAtISwERCAtFEgx6Rzp0cD4FUgApIDlwRx5XVR8mEjFsaidlcXl4NCx 2b1sAHFMLQ0VIBB8MGVgCEUNcGQlAQkIFVwJeHRdXWRtUXQAJV1gDBAoGBAsKUUICHkYHDVEcCx9 MARRWFVBcW15DAAFMXx9ETREcFVtaQxgcVgUdSl0FCFcMBBRVWUh2MTN2aCMxbWolZWoRDEBcTB4 cAx9UHxgCQAkUFBNBQBpQUVoLTFxsaiVncXl4NCx2MQgcHFdBVkUKEgYOVlNeGVxSFxsNXh4NCjY ECQhbXgIefhUBT1gCDXopGAoMRwMxfGtZPVBUHhl6KRgKDDQsdjMzdGgjMWxqCQ0FDQgOA1lGRAN GREMDB0QGAlcXRktZYkYEGExDGEVoBBgVEVpLKX1aBxxQMWxqJ2VxeXg0LHZzWwAcU0JWRQoIEBA UWEUFRR0HEVAfBx5NSwIcV1lNH11eFQYMXQUZUQwfHxcbSwReXhULUB8DGEI6FhQAGVkFVEEHaCM xbmolZXF5eDQxEVxLWR1QVB4ZCBcUCA1RXwJxVAYHTlAPGQsKAx54NCxyMTN0aCMxbHIlZXF7eDQ nAbOD460TYaxz5rvPHU6aKBw_" target="_blank"> If this email is not spam, click here to submit the signatures to FortiGuard - AntiSpam Service. Dear Justin, Thanks a lot for your response. Neda - Original Message - From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Sun, 15 Jul 2018 23:09:11 +0430 (IRDT) Subject: [Spam-FG] Re: [gmx-users] Negative pressure in NVT simulation http://nospammer.net/SubmitSpam/submitspam.php?id=I3RWARoweXYADkhffkN1 WA__=e3g1*tJ118poIzFkaiVlc3l4NCx2MTMqAFdFHFAKShwYFkFNGh9UBgdOUA8ZCwoDHld QQxVEXhEGV1AYA0oLXhoNRl4TX0dbHVBUHkdCEBgdHRtBEkEeGxhXWAMEVksZDRVYDxheXVkNUkQ FBkwHAxANWQEbVTN0aCExbGolZXF5d15NGlReHx1PcRoeCwAVDHg0LHQxM3RpIzFscU0RBQlCGwM BRkRaHEtUAA9IDgQVFFVOWFJcGWgjMW5qJWVxeXg0Fx5FRwRSDB4bHVJLFgsXWU0VQh0bGkQePx9 VFR4LDBthF1hfHQZEbiADVhECVj95dFtkQBEaUG4gA1YRcXl4Nix2MTN0aCMdBB5RFUtWV0NbAR9 UBgdOUA8ZCwoDHldnWQZBXAYcDHwNA0kMHx4neEUFRUB0aCMzbGolZXF5eHZEAkVDB1IMHgELTAk dEAtAAgVIQFoDV1lCGUBKHBgRWEEXXxwYAVBFBQRDCl4eCltBF1JAWgdRVjMNSB1cDAtRXgUxM3R qIzFsaiVlcWQfWVRbREARGlAcHg9UEBQKDHRLBF5eFQtQHwMYQmVxeXw0LHYxM3RoOzFsaidlcX* QXtr1BsjkCP*XyL2dAAIh5g__" target="_blank"> If this email is not spam, click here to submit the signatures to FortiGuard - AntiSpam Service. On 7/15/18 2:32 PM, Neda Rafiee wrote: ; energygrps = LYS LEU VAL PHE1 PHE2 ALA GLU ASP NaB ClB OXB OSil OGem OMB SIB SiSil SiGem HSil HGem OW HW energygrp_table = NaB OXB NaB OSil NaB OGem NaB OMB OMB OW OW SIB OW SiSil OW SiGem OW HSil OW HGem HW OMB HW OXB OW OSil OW OGem HW OSil HW OGem OXB OW freezegrps = SIB OXB OMB SiSil OSil SiGem OGem freezedim = Y Y Y Y Y Y Y Y Y
[gmx-users] [Spam-FG] Re: [Spam-FG] Re: Negative pressure in NVT simulation
If this email is not spam, click here to submit the signatures to FortiGuard - AntiSpam Service. Dear Justin, Thanks a lot for your response. Neda - Original Message - From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Sun, 15 Jul 2018 23:09:11 +0430 (IRDT) Subject: [Spam-FG] Re: [gmx-users] Negative pressure in NVT simulation If this email is not spam, click here to submit the signatures to FortiGuard - AntiSpam Service. On 7/15/18 2:32 PM, Neda Rafiee wrote: > ; > energygrps = LYS LEU VAL PHE1 PHE2 ALA GLU ASP NaB ClB OXB OSil OGem OMB SIB SiSil SiGem HSil HGem OW HW > energygrp_table = NaB OXB NaB OSil NaB OGem NaB OMB OMB OW OW SIB OW SiSil OW SiGem OW HSil OW HGem HW OMB HW OXB OW OSil OW OGem HW OSil HW OGem OXB OW > > freezegrps = SIB OXB OMB SiSil OSil SiGem OGem > freezedim = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y You're not using energy group exclusions, which the manual recommends when freezing: "To avoid spurious contributions to the virial and pressure due to large forces between completely frozen atoms you need to use energy group exclusions, this also saves computing time." http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#non-equilibrium-md Freezing is a very severe artificial perturbation, so you will have to use hacks like that if you intend to do a simulation with so many things frozen. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Negative pressure in NVT simulation
Dear Gromacs users, I have a system part of which is frozen in three dimensions, so I cannot do an NPT. To add solvent to my system, I used solvate but since I am using a user-defined vdwradii.dat to inhibit water enter my solid slab (my slab has a thickness about 3 nm), after some steps I understood that density of water is less than 1000 and so I calculated available volume that water molecules can be added to my box by subtravting the volume of my slab and then I used "gmx insert-molecules" command to add as much water molecules as required to get a density of 1000 Kg/m^3. Now, I am doing NVT and I get correct density for water but I see the pressure in my system is a very large negative number (minus ten to power 24). I want to discuss with you if it is a real problem in my system or not! I am using these mdp options: constraints = none constraint_algorithm = LINCS lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 integrator = md emstep = 0.0001 emtol = 50.0 ; ; Center of mass removal -- comm_mode = none; linear; Change for no pbc comm_grps = system; nstcomm = 10; freq of center of mass removal ; ; Time steps -- dt = 0.001 ;1 fs nsteps = 100 ;1 ns ; ; Output control --- nstxout = 1 ; freq of coord output to trr nstvout = 1 ; freq of velocity output to trr nstfout = 0 ; freq of force output to trr nstlog = 1 ; freq of output to log file nstenergy = 1 ; default of -1 sets equal to nstlist nstxtcout = 1 ; freq of coord output to xtc ; ; Neighbor list and pbc's -- cutoff-scheme = group nstlist = 10; default is 10 -- try more frequent ns_type = grid ; simple (for no pbc) or grid ; pbc = xyz ; CHANGE periodic_molecules = no ; ; Interaction parameters --- rlist = 1 rlistlong = 1 rcoulomb= 1 ; coulombtype = PME epsilon_r = 1 ; vdwtype = user; cut-off rvdw= 1 DispCorr= no ; no or EnerPres ; energygrps = LYS LEU VAL PHE1 PHE2 ALA GLU ASP NaB ClB OXB OSil OGem OMB SIB SiSil SiGem HSil HGem OW HW energygrp_table = NaB OXB NaB OSil NaB OGem NaB OMB OMB OW OW SIB OW SiSil OW SiGem OW HSil OW HGem HW OMB HW OXB OW OSil OW OGem HW OSil HW OGem OXB OW freezegrps = SIB OXB OMB SiSil OSil SiGem OGem freezedim = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y ; ; temperature coupling is on -- Tcoupl = v-rescale ;or v-rescale berendsen nose-hoover tau_t = 0.3 tc-grps = System ref_t = 300.0 ; Pressure coupling is not on -- Pcoupl = no ; no berendsen Parrinello-Rahman tau_p = 4 pcoupltype = anisotropic ; isotropic anisotropic compressibility = 10.e-5 10.e-5 10.e-5 0.0 0.0 0.0 ref_p = 1.0 1.0 1.0 0.0 0.0 0.0 ; distance restraint force constant ;disre = simple ;disre_fc= 1 ; Generate velocites --- gen_vel = yes gen_temp= 300.0 gen_seed= 173529 [ahmadabadi_i.ch.sharif@compute-0-1 1-1_max_ROG_over_Sil]$ cat run.mdp constraints = none constraint_algorithm = LINCS lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 integrator = md emstep = 0.0001 emtol = 50.0 ; ; Center of mass removal -- comm_mode = none; linear; Change for no pbc comm_grps = system; nstcomm = 10; freq of center of mass removal ; ; Time steps -- dt = 0.001 ;1 fs nsteps = 100 ;1 ns ; ; Output control --- nstxout = 1 ; freq of coord output to trr nstvout = 1 ; freq of velocity output to trr nstfout = 0 ; freq of force output to trr nstlog = 1 ; freq of output to log file nstenergy = 1 ; default of -1 sets equal to nstlist nstxtcout = 1 ; freq of coord output to xtc ; ; Neighbor list and pbc's -- cutoff-scheme = group nstlist = 10; default is 10 -- try
Re: [gmx-users] GPU+Energy Groups
Hi Mark, Thanks a lot for your help. Actually, in my case tables are defined for non-bonded LJ interactions. Anyway, I need them since all we did were on defining those tables :) Thanks again, Neda - Original Message - From: Mark Abraham To: gmx-us...@gromacs.org Sent: Fri, 06 Jul 2018 17:23:30 +0430 (IRDT) Subject: Re: [gmx-users] GPU+Energy Groups Hi, You can't ever use a tabulated short-range interaction on a GPU in GROMACS at this time. Mark On Fri, Jul 6, 2018 at 10:55 AM Neda Rafiee wrote: > Dear GMX-Users, > I am going to use GPU acceleration for my simulations but since I have > some energy tables for LJ interactions, and I am using cut-off scheme=group > instead of Verlet, I receive these notes: > > "NOTE: GPU(s) found, but the current simulation can not use GPUs > To use a GPU, set the mdp option: cutoff-scheme = Verlet > Multiple energy groups is not implemented for GPUs, falling back to the > CPU. For better performance, run on the GPU without energy groups and then > do gmx mdrun -rerun option on the trajectory with an energy group .tpr file. > Using 1 MPI process" > > Is it reasonable to do my simulations using GPU and rerun it using > energy-groups? How will those non-bonded interaction tables be taken into > account in my first simulations with GPU? > Thanks in advance. > Neda > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GPU+Energy Groups
Dear GMX-Users, I am going to use GPU acceleration for my simulations but since I have some energy tables for LJ interactions, and I am using cut-off scheme=group instead of Verlet, I receive these notes: "NOTE: GPU(s) found, but the current simulation can not use GPUs To use a GPU, set the mdp option: cutoff-scheme = Verlet Multiple energy groups is not implemented for GPUs, falling back to the CPU. For better performance, run on the GPU without energy groups and then do gmx mdrun -rerun option on the trajectory with an energy group .tpr file. Using 1 MPI process" Is it reasonable to do my simulations using GPU and rerun it using energy-groups? How will those non-bonded interaction tables be taken into account in my first simulations with GPU? Thanks in advance. Neda -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] non-bounded parameters
Dear gmx-users, I got the following note while producing my run input file: "Generated 279 of the 1953 non-bonded parameter combinations" I should say that I am using a recently developed force field and I know that some third-body potentials are not defined in it. I am not sure if it is the main reason or not and how to be sure everything is in the right place. Can anyone give me a hint ? Thanks in advance. Neda -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Protein-surface Binding energy
Dear Gromacs users, I have a question regarding the calculation of binding energy for protein-surface interactions. I found that for protein-ligand systems, LIE method was suggested but what about protein-surface? if I have done two simulations, one with protein attached to the surface and the other with only protein in water !? Does anyone know whether I can use my protein-in-water and protein-surface simulations to do so? Or should I use my protein-surface and surface-water simulations? My surface is freezed except that some hydrogen atoms on top of it. Thanks in advance, Neda -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] dipole moment for one residue of the whole protein
Dear users, I want to calculate Phenyl dipole moment from my traj.trr file but my trajectory does not contain mass and charge. I used "gmx dipole " command for this purpose but it gives me error that Phenyl is not a whole molecule (actually because it is part of my protein which is a molecule in its own). I also used Plumed and wrote mass and charges in the file "mcfile" to define charges of atoms: plumed driver --mc mcfile --plumed Plumed_Inputs_7mar18/dipole.dat --mf_trr traj_01234_pbc.trr it does not give any error but just writing "nan" instead of giving a meaningful dipole moment. Can you help me with this? Thanks in advance. NEDA -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] cannot flush logfile
Dear Users, I have a problem with running my simulation on cluster. Actually the error says : "Fatal error:Cannot flush logfile - maybe you are out of disk space?" while I have plenty of free disk space. I have also tried with different number of nodes and processors per node and I encountered the same problem. I am using gromacs v.5.0 with the following modules: module load intel/2013 module load openmpi/1.6.5/intel/2013 module load gromacs/5.0-rc1 and the following command: " mpirun gmx_mpi_d mdrun -cpt -1 -s run.tpr -o run.trr -g run.log -e run.edr -c run.gro " Can anyone help me ??? Thanks in advance. Neda -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Minimization problem
Dear Users, I have a problem in energy minimization step. Actually I have some groups of atoms that are freezed and also a chain of protein in water. I want the following items: constraints = none integrator = steep emstep = 0.0001 emtol = 500.0 nsteps = 50 ; Neighbor list and pbc's -- cutoff-scheme = group nstlist = 1; default is 10 -- try more frequent ns_type = grid ; simple (for no pbc) or grid ; pbc = xyz ; CHANGE periodic_molecules = no ; ; Interaction parameters --- rlist = 1 rlistlong = 1 rcoulomb= 1 ; coulombtype = PME epsilon_r = 1 ; vdwtype = user; cut-off rvdw= 1 but after just 6000 steps it gives me this error: Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 500 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 53429 steps, but did not reach the requested Fmax < 500. Potential Energy = 2.46705107676305e+14 Maximum force = 9.69602643026733e+08 on atom 9415 Norm of force = 1.70746371816015e+07 Would you please help me understand where the problem is ?! Thanks Neda -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] converting xtc to pdb without need to tpr file using trjconv
Thanks a lot Justin Neda - Original Message - From: Justin Lemkul <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Mon, 07 Aug 2017 19:08:05 +0430 (IRDT) Subject: Re: [gmx-users] converting xtc to pdb without need to tpr file using trjconv On 8/7/17 2:42 AM, Neda Rafiee wrote: > Dear users, > Anyone knows how can I use trjconv to convert an xtc file to pdb format > without need to tpr file ? trjconv does accept PDB files to -s but then you don't get PBC or connectivity information. You need to provide some source of atom and residue names, because none of that is in an XTC file. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] converting xtc to pdb without need to tpr file using trjconv
Dear users, Anyone knows how can I use trjconv to convert an xtc file to pdb format without need to tpr file ? Thanks, Neda -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error in nvidia cuda installation
Thanks a lot Stephane and Nikhil Regards, Neda - Original Message - From: Stephane TELETCHEA <stephane.teletc...@univ-nantes.fr> To: gromacs org gmx-users <gromacs.org_gmx-users@maillist.sys.kth.se> Sent: Tue, 04 Jul 2017 18:47:56 +0430 (IRDT) Subject: Re: [gmx-users] error in nvidia cuda installation You have to close all X window, disconnect, then go to the console using ctrl+alt+F1, an then: 1) turn off the xserver and/or the login manager: sudo service lightdm stop (in Ubuntu) sudo service gdm stop (Mint) 2) performs the steps again, it should work now 3) reboot (the initrd/initramfs is rebuilt to remove kms which is incompatible between NVIDIA and nouveau) If not, please post again the error message on the list. Best, Stéphane Le 04/07/2017 à 14:12, Neda Rafiee a écrit : > Would you please help me detecting the problem of CUDA with my system? > I don't know if the problem is related to the Internet or another > thing. What does the error mean by "X server" ? > Neda -- Lecturer, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error in nvidia cuda installation
Dear Stephane, I followed the instructions in this link: http://www.steletch.org/spip.php?article89 With ctrl+alt+f1 I went to console, then I logged in and typed: sudo service lightdm stop there was an error : Unit lightdm.service not loaded Then I typed: sudo rmmmod nvidia I got another error : Module nvidia not currently loaded After that I typed: sudo apt-get --purge remove cuda* nvidia* and using "sudo apt autoremove" I removed the suggested files. still in console, I typed : sh cuda_8.0.61_375.26_linux.run --toolkitpath=/opt/apps/pkg/cuda/8.0.61 -> Accept default location -> accept the DRIVER ...And suddenly the page was changed to a very long description that at the end asked me to accept/decline or quit the session. When I chose "decline" or "quit", it would come out of the script, but when I chose "accept", it continued to ask me lots of questions about the location to be installed, OpenGL option, using -Xconfig or not, and many others with yes/no options. When I answered to all of the questions, a sentence appeared : "Installing the NVIDIA display driver..." And after a while, it said: "It appears that an x server is running. Please exit X before installation. If you are sure that X is not running, but still are getting this error, please delete any X lock file in /tmp. " And then: "Driver installation failed !" Would you please help me detecting the problem of CUDA with my system? I don't know if the problem is related to the Internet or another thing. What does the error mean by "X server" ? Neda -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error in nvidia cuda installation
Dear Stephane, I tried to install drivers and cuda as was syggested in the link you sent me yesterday. I go through the first steps, but after choosing to install cuda and replying yes to all the questions, I got an error indicating that drivers installation failed. What should I do now? Thanks Neda - Original Message - From: Stéphane Téletchéa <stephane.teletc...@univ-nantes.fr> To: gromacs org gmx-users <gromacs.org_gmx-users@maillist.sys.kth.se> Sent: Mon, 03 Jul 2017 22:20:31 +0430 (IRDT) Subject: Re: [gmx-users] error in nvidia cuda installation Le 03/07/2017 à 17:48, Neda Rafiee a écrit : > I am going to install GROMACS 5.1.4 which is enabled for parallelization, so > I tried to install Cuda Nvidia as it is suggested in the gromacs website. I > am using Linux Mint 18.1 Dear Neda, GROMACS + CUDA wroks best if you install the driver and nvidia using the same download. This works: http://www.steletch.org/spip.php?article89 Long story short: install NVIDIA cuda + the driver from the very same package. Be sure to remove all distribution-provided packages (sudo apt-get remove --purge *nvidia*, --purge IS important). Best, Stéphane -- Lecturer, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error in nvidia cuda installation
Dear Mark and Stephane, Thanks a lot for your very usefull advices. Neda - Original Message - From: Stéphane Téletchéa <stephane.teletc...@univ-nantes.fr> To: gromacs org gmx-users <gromacs.org_gmx-users@maillist.sys.kth.se> Sent: Mon, 03 Jul 2017 22:20:31 +0430 (IRDT) Subject: Re: [gmx-users] error in nvidia cuda installation Le 03/07/2017 à 17:48, Neda Rafiee a écrit : > I am going to install GROMACS 5.1.4 which is enabled for parallelization, so > I tried to install Cuda Nvidia as it is suggested in the gromacs website. I > am using Linux Mint 18.1 Dear Neda, GROMACS + CUDA wroks best if you install the driver and nvidia using the same download. This works: http://www.steletch.org/spip.php?article89 Long story short: install NVIDIA cuda + the driver from the very same package. Be sure to remove all distribution-provided packages (sudo apt-get remove --purge *nvidia*, --purge IS important). Best, Stéphane -- Lecturer, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] error in nvidia cuda installation
Dear users, I am going to install GROMACS 5.1.4 which is enabled for parallelization, so I tried to install Cuda Nvidia as it is suggested in the gromacs website. I am using Linux Mint 18.1 I tried to download Cuda toolkit from its website but the link seems not to work properly at the present time. Here it is: http://developer2.download.nvidia.com/compute/cuda/8.0/secure/Prod2/local_installers/cuda-repo-ubuntu1604-8-0-local-ga2_8.0.61-1_amd64.deb?vmYFoBWDG3rPn44_PXesEZzhZKZBfQhZUlE0ejZIsLsGUAyLFN5AVFpzvAECUUPTxrKQY78vMi1MEyMHXyYaoupnSvADVKrj_DDrxr4eeE2OJUgAFzbT4fVBHMQzAAuc_DiJsX1S6JwRlyeOsS4XbS-uHan2fLyrDDCr03z0AnFyffKbewEUrFyrCz57hrLGTe9pTeniMd87kBD4mXqZ9AXr1g I also tried downloading via " apt-get install nvidia-cuda-toolkit ", as suggested in the link below: https://askubuntu.com/questions/640577/install-cuda-7-0-on-ubuntu-14-04-2 but after entering " sudo apt-get install nvidia-XXX nvidia-prime ", I got an error indicating "E: Unable to locate package nvidia-XXX " Anyone knows what should I do? Thanks. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] replica exchange
Dear All, I am doing replica exchange for a peptide in water and I used the following command to run my system: mpirun -np 4 mdrun_mpi -v -multidir equil[0123] but I encountered with an error saying: HYDU_create_process (utils/launch/launch.c:75): execvp error on file mdrun_mpi (No such file or directory) Can anyone help me find out the problem? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] LINCS
Thanks Joao. My problem was solved after I changed mdrun options. - Original Message - From: "João Henriques" <joao.m.a.henriq...@gmail.com> To: gmx-us...@gromacs.org Sent: Sunday, April 9, 2017 4:44:22 PM Subject: Re: [gmx-users] LINCS Dear Neda, I'm not sure I appreciate the ellipses after "thanks". After all, I took some of my personal time - on a Sunday - to do your work and Google search for the key words in your error message. Plus, I sent you the link and pointed you to the right section, which contains a crystal clear explanation of some of possible reasons for this error. In any case, to avoid having someone think I am being purposely condescending, I will tell you that your system cannot be decomposed into the requested 16 MPI ranks. This is likely due to the fact that it is too small and decomposing the simulation box into 16 parts would break one or more of the following things: (i) the size of the largest charge group or bonded interaction, (ii) the largest of rvdw, rlist and rcoulomb, or (iii) other parameters associated with bond constraints. You need to experiment using a lower number of MPI ranks. Then again, without any information about your system, Gromacs version, etc, it is impossible to pinpoint the exact reason. Best regards, /J On Sun, Apr 9, 2017 at 1:38 PM, Neda Rafiee <neraf...@ipm.ir> wrote: > Thanks > > - Original Message - > From: "João Henriques" <joao.m.a.henriq...@gmail.com> > To: gmx-us...@gromacs.org > Sent: Sunday, April 9, 2017 3:37:46 PM > Subject: Re: [gmx-users] LINCS > > Google is your friend, *always*. > > Please see the last section on: > > http://www.gromacs.org/Documentation/Errors > > /J > > On Sun, Apr 9, 2017 at 10:00 AM, Neda Rafiee <neraf...@ipm.ir> wrote: > > > Dear gmx-users, > > I have a problem in doing nv pequilibration for my pritein-water system, > I > > do not understand the error: > > There is no domain decomposition for 16 ranks that is compatible with the > > given box and a minimu$ > > Change the number of ranks or mdrun option -rcon or -dds or your LINCS > > settings > > Look in the log file for details on the domain decomposition > > > > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] LINCS
Thanks - Original Message - From: "João Henriques" <joao.m.a.henriq...@gmail.com> To: gmx-us...@gromacs.org Sent: Sunday, April 9, 2017 3:37:46 PM Subject: Re: [gmx-users] LINCS Google is your friend, *always*. Please see the last section on: http://www.gromacs.org/Documentation/Errors /J On Sun, Apr 9, 2017 at 10:00 AM, Neda Rafiee <neraf...@ipm.ir> wrote: > Dear gmx-users, > I have a problem in doing nv pequilibration for my pritein-water system, I > do not understand the error: > There is no domain decomposition for 16 ranks that is compatible with the > given box and a minimu$ > Change the number of ranks or mdrun option -rcon or -dds or your LINCS > settings > Look in the log file for details on the domain decomposition > > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] LINCS
Dear gmx-users, I have a problem in doing nv pequilibration for my pritein-water system, I do not understand the error: There is no domain decomposition for 16 ranks that is compatible with the given box and a minimu$ Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] NVE run
Thanks a lot Mark... Kind regards, Neda Rafieiolhosseini Ph.D. Student at Institute for Research in Fundamental Sciences(IPM), School of Nano, Tehran,Iran. - Original Message - From: "Mark Abraham" <mark.j.abra...@gmail.com> To: gmx-us...@gromacs.org Sent: Wednesday, March 29, 2017 2:38:54 PM Subject: Re: [gmx-users] NVE run Hi, There's no way to say. Those numbers would be more indicative of a problem if the system was small, or the simulation was short, but we don't know those (and there are many algorithm settings that contribute). What you really need is to know whether the quality of your observables is degraded over the time scale of the simulation; at best energy conservation is only a proxy for that. See thoughts at http://biorxiv.org/content/early/2016/10/24/083055 Mark On Wed, Mar 29, 2017 at 2:02 PM Neda Rafiee <neraf...@ipm.ir> wrote: > Dear gromax users, > I have already run my system under NVE condition with dt=2fs and I found > the energy drift about -7000 KJ/mol, then I repeated my simulation with > dt=1fs again and I found the drift about -1900 KJ/mol. Is it a reasonable > value or should I have a smaller drift? THANKS. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] NVE run
Dear gromax users, I have already run my system under NVE condition with dt=2fs and I found the energy drift about -7000 KJ/mol, then I repeated my simulation with dt=1fs again and I found the drift about -1900 KJ/mol. Is it a reasonable value or should I have a smaller drift? THANKS. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] RNEMD in Gromacs
Dear Gromacs users, Anyone knows about Reverse Non-Equilibrium Molecular Dynamics (RNEMD) in Gromacs? I know it is available in LAMMPS, but my system and all my works till now have been done in Gromacs. Is it easier to shift to LAMMPS or can I write the RNEMD method in Gromacs? I need this method to calculate thermal conductivity. Thanks in advance. Neda -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Adding water to specific part of a box
Thanks Victor! - Original Message - From: "Victor Rosas Garcia" <rosas.vic...@gmail.com> To: gmx-us...@gromacs.org Sent: Monday, February 13, 2017 9:30:12 PM Subject: Re: [gmx-users] Adding water to specific part of a box You could try resizing the box of your system with gmx editconf, so the box does not include the region below the bilayer, add solvent with either gmx insert-molecules or gmx solvate, and then use gmx editconf again to leave the box as it was before adding the solvent. Hope this helps Victor 2017-02-13 3:17 GMT-06:00 Neda Rafiee <neraf...@ipm.ir>: > I mean adding water above the membrane bilayer and not below it for > example. There is an option in VMD in Selection part, which allows the user > remove water molecules from z>(upper bond) and z<(lower bond), but I don't > know if there is any option which allows you insert water molecules like > that! > > > > - Original Message - > From: "Mohamad Koohi-Moghadam" <m.kooh...@gmail.com> > To: gmx-us...@gromacs.org > Sent: Monday, February 13, 2017 12:41:10 PM > Subject: Re: [gmx-users] Adding water to specific part of a box > > What do you mean by "specif part"? For example just in binding site of > protein-ligand and not in other part? > > On Mon, Feb 13, 2017 at 5:02 PM, Neda Rafiee <neraf...@ipm.ir> wrote: > > > Dear users, > > Any one knows how to add water molecules only to specific parts of a > > system in GROMACS? > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Adding water to specific part of a box
I mean adding water above the membrane bilayer and not below it for example. There is an option in VMD in Selection part, which allows the user remove water molecules from z>(upper bond) and z<(lower bond), but I don't know if there is any option which allows you insert water molecules like that! - Original Message - From: "Mohamad Koohi-Moghadam" <m.kooh...@gmail.com> To: gmx-us...@gromacs.org Sent: Monday, February 13, 2017 12:41:10 PM Subject: Re: [gmx-users] Adding water to specific part of a box What do you mean by "specif part"? For example just in binding site of protein-ligand and not in other part? On Mon, Feb 13, 2017 at 5:02 PM, Neda Rafiee <neraf...@ipm.ir> wrote: > Dear users, > Any one knows how to add water molecules only to specific parts of a > system in GROMACS? > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Adding water to specific part of a box
Dear users, Any one knows how to add water molecules only to specific parts of a system in GROMACS? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem with membrane simulation
Thanks Mark! it worked... - Original Message - From: "Mark Abraham" <mark.j.abra...@gmail.com> To: gmx-us...@gromacs.org Sent: Tuesday, February 7, 2017 7:20:28 PM Subject: Re: [gmx-users] Problem with membrane simulation Hi, You can fill your box before you concatenate. Mark On Tue, 7 Feb 2017 16:42 Neda Rafiee <neraf...@ipm.ir> wrote: > Dear GMX-USERS, > I have a major problem with building my system which contains two parallel > bilayers. If I use different servers such as CHARMM-GUI or ATB or any > other, I will have gro and top file and I can concatenate two bilayers into > one simulation box. But when I fill the box with water (using $gmx editconf > ... and $gmx solvate ...), I will have water all over the box, and it is > not desirable. I want to have water moleculed just above and under > bilayers. On the other hand, if I use Packmol software, I will get my > desirable coordinate file, but I cannot produce .top and .gro with pdb2gmx > according to what Lindahl suggest in this video: > https://www.youtube.com/watch?v=nwMiqP4g1Zo > Has anyone worked with Packmol for lipid bilayers? > Thanks > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problem with membrane simulation
Dear GMX-USERS, I have a major problem with building my system which contains two parallel bilayers. If I use different servers such as CHARMM-GUI or ATB or any other, I will have gro and top file and I can concatenate two bilayers into one simulation box. But when I fill the box with water (using $gmx editconf ... and $gmx solvate ...), I will have water all over the box, and it is not desirable. I want to have water moleculed just above and under bilayers. On the other hand, if I use Packmol software, I will get my desirable coordinate file, but I cannot produce .top and .gro with pdb2gmx according to what Lindahl suggest in this video: https://www.youtube.com/watch?v=nwMiqP4g1Zo Has anyone worked with Packmol for lipid bilayers? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Periodicity in x-y plane (Neda Rafiee)
Thanks Bjoern! Kind regards, Neda Rafieiolhosseini Ph.D. Student at Institute for Research in Fundamental Sciences(IPM), School of Nano, Tehran,Iran. - Original Message - From: "Björn Sommer" <bjo...@cellmicrocosmos.org> To: "gromacs org gmx-users" <gromacs.org_gmx-users@maillist.sys.kth.se> Sent: Monday, February 6, 2017 2:43:21 PM Subject: Re: [gmx-users] Periodicity in x-y plane (Neda Rafiee) Hi Neda, On 6/02/2017 8:43 am, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: > 6. Periodicity in x-y plane (Neda Rafiee) > > > > Message: 6 > Date: Mon, 6 Feb 2017 11:08:42 +0330 (IRST) > From: Neda Rafiee <neraf...@ipm.ir> > To: gmx-us...@gromacs.org > Subject: [gmx-users] Periodicity in x-y plane > Message-ID: <12473704.8815.1486366722721.javamail.r...@zmail.ipm.ir> > Content-Type: text/plain; charset=utf-8 > > Hi. I have already built a lipid bilayer and I want to create a box for it > and fill it with water. I used : > $ gmx editconf -f renumber.gro -o newbox.gro -c -box 8 8 14 -bt triclinic > and after that I used: > $ gmx solvate -cp newbox.gro -cs tip4p.gro -o solvated.gro -p topol.top > > but when I see solvated.gro in VMD, in periodicity , I check x +x or y +y > direction, I see man water molecules between adjacent neighbors in x-y > direction and it destroy the periodicity of my membrane in x-y plane, while I > want to have water only in the upper and lower sides of the membrane. What > should I do? > > Please play around with this: http://www.cellmicrocosmos.org/Cmforum/viewtopic.php?f=21=641 Shortly, in VMD use in the Graphical Representations window a selection like not ((resname 'W' 'NA+') and within 5.5 of (not resname 'W' 'NA+')) See the previous link for more info. Basically, make sure that no water is inside the membrane but also that the distance between the water bath and the head groups is not too small, otherwise the box will shrink during simulation and the membrane might deform a little bit. After that, use the regular PDB export and make sure to select the actual selection in the export window!/ / Have fun! Bjorn / / -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Membrane cutt-offs
Thanks Catarina! Kind regards, Neda Rafieiolhosseini Ph.D. Student at Institute for Research in Fundamental Sciences(IPM), School of Nano, Tehran,Iran. - Original Message - From: "Catarina A. Carvalheda dos Santos" <c.a.c.dossan...@dundee.ac.uk> To: "Discussion list for GROMACS users" <gmx-us...@gromacs.org> Sent: Monday, February 6, 2017 1:55:27 PM Subject: Re: [gmx-users] Membrane cutt-offs Hi, Just check the paper corresponding to the lipid force field you want to use. Cheers, On 6 February 2017 at 06:41, Neda Rafiee <neraf...@ipm.ir> wrote: > Hi! > I have a question regarding to cut-off values for membranes. I know that > using usual cut-offs is not appropriate for systems including membrane. > Where can I find the appropriate values? > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > The University of Dundee is a registered Scottish Charity, No: SC015096 > -- Catarina A. Carvalheda PhD Student Computational Biology Division SLS & SSE University of Dundee DD1 5EH, Dundee, Scotland, UK -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Periodicity in x-y plane
Hi. I have already built a lipid bilayer and I want to create a box for it and fill it with water. I used : $ gmx editconf -f renumber.gro -o newbox.gro -c -box 8 8 14 -bt triclinic and after that I used: $ gmx solvate -cp newbox.gro -cs tip4p.gro -o solvated.gro -p topol.top but when I see solvated.gro in VMD, in periodicity , I check x +x or y +y direction, I see man water molecules between adjacent neighbors in x-y direction and it destroy the periodicity of my membrane in x-y plane, while I want to have water only in the upper and lower sides of the membrane. What should I do? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Membrane cutt-offs
Hi! I have a question regarding to cut-off values for membranes. I know that using usual cut-offs is not appropriate for systems including membrane. Where can I find the appropriate values? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] having problem with topology file
Thanks Justin! Yaah. I found the appropriate force field in related section in ATB website with this name: gromos54a7_atb.ff.tar And this is what I wanted! Thanks a lot - Original Message - From: "Justin Lemkul" <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Sunday, January 29, 2017 5:46:34 PM Subject: Re: [gmx-users] having problem with topology file On 1/28/17 12:57 PM, Neda Rafiee wrote: > Hi. I have problem in building topology file for my system which is a > pre-equilibrated membrane adopted from ATB . I have the .gro file and I need > to have the topology file to do rest of my simulation. I did not find the top > file in ATB website . So I am using g_x2top to do this, but I face with this > error: > > Fatal error: > No or incorrect atomname2type.n2t file found (looking for > ./gromos45a3_lipid.ff) > > I am using altered Gromos45a3.ff which I added Burger lipid.itp , dppc.itp > and dopc.itp parameters to it according to the tutorial for "KALP-15 in DPPC" > bu Justin Lemkul. If ATB is providing you with files for lipids, it should also give you the lipid parameters. Otherwise, consult the literature for a proper topology, rather than trying to reinvent one with x2top. GROMOS force fields do not have .n2t files built in, so you would have to build a correct one yourself, which still requires you to know everything about the topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] having problem with topology file
Hi. I have problem in building topology file for my system which is a pre-equilibrated membrane adopted from ATB . I have the .gro file and I need to have the topology file to do rest of my simulation. I did not find the top file in ATB website . So I am using g_x2top to do this, but I face with this error: Fatal error: No or incorrect atomname2type.n2t file found (looking for ./gromos45a3_lipid.ff) I am using altered Gromos45a3.ff which I added Burger lipid.itp , dppc.itp and dopc.itp parameters to it according to the tutorial for "KALP-15 in DPPC" bu Justin Lemkul. Thanks, Neda -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
