Re: [gmx-users] compressibility values in coarse grained simulations
Hi, On Fri, Jan 3, 2020 at 12:04 PM Deepanshi . wrote: > Dear all, > > I am using the coarse-grained molecular dynamics simulation to study > membranes. In the production run .mdp file, to control the pressure I am > using semiisotropic in the Pcoupltype option. I wanted to ask how many > values I should give to compressibility and ref_p 2 values (see http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=semiisotropic#mdp-value-pcoupltype=semiisotropic ) > and what will happen if I > give more or fewer values than the actual values? > I do not know. But 1) you may get an error when running grompp 2) you could look at md.log to see what is the taken setting. > Also, I wanted to ask that for coarse-grained simulations the value for > compressibility should be 3e-5 or 4e-5? > Some CG models (like for example MARTINI) provides specific setting for pressure coupling. If you are using an already developed CG model, I suggest to refer to the authors suggestions. Best regards Alessandra > > Thanks. > > Regards, > Deepanshi. > -- > 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] compressibility values in coarse grained simulations
Dear all, I am using the coarse-grained molecular dynamics simulation to study membranes. In the production run .mdp file, to control the pressure I am using semiisotropic in the Pcoupltype option. I wanted to ask how many values I should give to compressibility and ref_p and what will happen if I give more or fewer values than the actual values? Also, I wanted to ask that for coarse-grained simulations the value for compressibility should be 3e-5 or 4e-5? Thanks. Regards, Deepanshi. -- 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] compressibility values in coarse grained simulations
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-value-pcoupltype=semiisotropic 2 for each. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Fri, 3 Jan 2020 at 22:03, Deepanshi . wrote: > Dear all, > > I am using the coarse-grained molecular dynamics simulation to study > membranes. In the production run .mdp file, to control the pressure I am > using semiisotropic in the Pcoupltype option. I wanted to ask how many > values I should give to compressibility and ref_p and what will happen if I > give more or fewer values than the actual values? > Also, I wanted to ask that for coarse-grained simulations the value for > compressibility should be 3e-5 or 4e-5? > > Thanks. > > Regards, > Deepanshi. > -- > 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] compressibility values in coarse grained simulations
Dear all, I am using the coarse-grained molecular dynamics simulation to study membranes. In the production run .mdp file, to control the pressure I am using semiisotropic in the Pcoupltype option. I wanted to ask how many values I should give to compressibility and ref_p and what will happen if I give more or fewer values than the actual values? Also, I wanted to ask that for coarse-grained simulations the value for compressibility should be 3e-5 or 4e-5? Thanks. Regards, Deepanshi. -- 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] compressibility
On 9/11/19 6:50 AM, m g wrote: Dear Justin,I'm simulating 400 molecules of naphthalene in NPT ensemble at gas phase. Is it true that I set water compressibility in .mdp file? What must I do? Should I look for naphthalene isothermal compressibility in articles to use it?Thanks,Sana If you're simulating in the gas phase, you shouldn't be using an NPT ensemble and therefore the compressibility is irrelevant. Use NVT. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 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.
[gmx-users] compressibility
Dear Justin,I'm simulating 400 molecules of naphthalene in NPT ensemble at gas phase. Is it true that I set water compressibility in .mdp file? What must I do? Should I look for naphthalene isothermal compressibility in articles to use it?Thanks,Sana -- 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] Compressibility and Tau-p
Dear all, I wonder how to choose reasonable quantities for compressibility and Tau-p parameters for a polymer system? Thank you. Alex -- 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] compressibility
Dear all, As you know the compressibility for water at 1 atm and 300 K is 4.5e-5 [bar -1], I wonder how to choose proper compressibility for other materials? I have two types of polymer inside water. Also, I see sometimes the compressibility is indicated by one, two or three number in the form of "compressibility = C1 C2 C3, then if those C1, C2 and C3 are the compressibility in three geometrical directions of x,y,z for the whole system, or just the compressibility for three type of material existing in the system? Thank you. Alex -- 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] Compressibility in .mdp
Dear Gromacs users I have a question about the concept of the compressibility factor in .mdp file. suppose I assign Compressibility in X direction equal to zero. does this mean that the atoms in X direction cannot move at all or just the size of the� simulation box� in this direction remain unchanged?� I really appreciate it if anyone can help me. best regards, Ali == Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir) Department of Mechanical Engineering Sharif University of Technology, Tehran, Iran -- 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] compressibility
Hi, I simulate a molecule in NPT ensemble, which I can not find any experimental data about it's compressibility, what should I put in .mdp file for it's compressibility in pressure coupling? Best regards -- 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] compressibility
Thank you Michael! Best regards On Fri, Jun 12, 2015 at 1:19 PM, Michael Shirts mrshi...@gmail.com wrote: The 'compressibility' in the pressure coupling is not actually the compressibility of the fluid; it's another way to write the mass of the fictitious piston. It affects the inertia of the piston and the period of the oscillations of the box, but won't affect the magnitude of fluctuations of the box. Having a value near the compressibility of the fluid, I believe, minimizes the chances of unstable simulations and weird resonances, but is not required. On Fri, Jun 12, 2015 at 3:12 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Hi, I simulate a molecule in NPT ensemble, which I can not find any experimental data about it's compressibility, what should I put in .mdp file for it's compressibility in pressure coupling? Best regards -- 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] compressibility
The 'compressibility' in the pressure coupling is not actually the compressibility of the fluid; it's another way to write the mass of the fictitious piston. It affects the inertia of the piston and the period of the oscillations of the box, but won't affect the magnitude of fluctuations of the box. Having a value near the compressibility of the fluid, I believe, minimizes the chances of unstable simulations and weird resonances, but is not required. On Fri, Jun 12, 2015 at 3:12 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Hi, I simulate a molecule in NPT ensemble, which I can not find any experimental data about it's compressibility, what should I put in .mdp file for it's compressibility in pressure coupling? Best regards -- 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.
