[gmx-users] REMD Simulation for a system at different Concentration
Dear all, I am planning to do REMD for a system containing Protein, Urea, Osmolyte and water, I want to generate the temperature replica. So the REMD temperature generator asks for number of water molecules only, but here in my case there are something more in the system, So is it fine that I can proceed further with this? My next query is that I am going to do the REMD in two different concentration, for each concentration the number of water molecules will be different, so my temperature replica also will be different for the same system at different concentration. So I want to know whether REMD can be effective in the case of a system at different concentration (number of water molecules changes, so temperature replica will be different) having Protein, Urea, Osmolyte and water? Can someone please help me with this.. Thanks in advance... -Ligesh -- 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] REMD Showing Zero Exchange Probability
Sorry for the delay..Thank you Mark.. On Sat, Jul 21, 2018 at 2:09 AM, Mark Abraham wrote: > Hi, > > You can't arbitrarily choose both the temperature range and number of > replicas and get non-zero exchange probability. See > https://pubs.acs.org/action/showCitFormats?doi=10.1021%2Fct800016r. For a > given average exchange probability, choose a range and thus the number of > replicas, or the number of replicas and thus the range. > > Mark > > On Fri, Jul 20, 2018, 10:39 Ligesh Lichu wrote: > > > Dear all, > > I have performed REMD for a system containing Protein, Reline, Urea > and > > Water in the temperature range 290 to 450 K consist of 16 replicas out of > > 47 replicas generated by REMD temperature generator. But after the MD > > simulation the exchange probability is zero. I have used position > > restraints for reline, urea and protein. Is there any chance that > position > > restraints cause the exchange probability to be zero? I have one more > > query that, the REMD temperature generator produced around 45 to 54 > > replicas for my system in the required temperature range. But I have only > > 80 processors to do the job, So is it necessary to choose the consecutive > > temperature replicas given by the REMD temperature generator or I can > skip > > some temperatures in between? > > > > If I am using the equation *Ti = T0 exp (k* i)*, what determines the > value > > of 'k' how it affects the exchange probability? How can I choose the > value > > of 'k' for an arbitrary system? > > > > Thanks in advance... > > -- > > 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] REMD Showing Zero Exchange Probability
I have tried an exchange every 2 ps. That is every 1000 steps. On Fri, Jul 20, 2018 at 5:34 PM, Smith, Micholas D. wrote: > How frequently are you trying to exchange? > > === > Micholas Dean Smith, PhD. MRSC > Post-doctoral Research Associate > University of Tennessee/Oak Ridge National Laboratory > Center for Molecular Biophysics > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Ligesh > Lichu > Sent: Friday, July 20, 2018 4:39 AM > To: gmx-us...@gromacs.org > Subject: [gmx-users] REMD Showing Zero Exchange Probability > > Dear all, > I have performed REMD for a system containing Protein, Reline, Urea and > Water in the temperature range 290 to 450 K consist of 16 replicas out of > 47 replicas generated by REMD temperature generator. But after the MD > simulation the exchange probability is zero. I have used position > restraints for reline, urea and protein. Is there any chance that position > restraints cause the exchange probability to be zero? I have one more > query that, the REMD temperature generator produced around 45 to 54 > replicas for my system in the required temperature range. But I have only > 80 processors to do the job, So is it necessary to choose the consecutive > temperature replicas given by the REMD temperature generator or I can skip > some temperatures in between? > > If I am using the equation *Ti = T0 exp (k* i)*, what determines the value > of 'k' how it affects the exchange probability? How can I choose the value > of 'k' for an arbitrary system? > > Thanks in advance... > -- > 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] REMD Showing Zero Exchange Probability
Dear all, I have performed REMD for a system containing Protein, Reline, Urea and Water in the temperature range 290 to 450 K consist of 16 replicas out of 47 replicas generated by REMD temperature generator. But after the MD simulation the exchange probability is zero. I have used position restraints for reline, urea and protein. Is there any chance that position restraints cause the exchange probability to be zero? I have one more query that, the REMD temperature generator produced around 45 to 54 replicas for my system in the required temperature range. But I have only 80 processors to do the job, So is it necessary to choose the consecutive temperature replicas given by the REMD temperature generator or I can skip some temperatures in between? If I am using the equation *Ti = T0 exp (k* i)*, what determines the value of 'k' how it affects the exchange probability? How can I choose the value of 'k' for an arbitrary system? Thanks in advance... -- 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.
