Re: [gmx-users] Free volume variation during the simulation
Is it an NPT simulation or NVT simulation? Arun On Wed, 6 May 2020, 9:27 am Mohamed Abdelaal, wrote: > Yes I measured both, the density and the free volume using gromacs. > > Since the free volume changes with respect to time, shouldn’t the density > also change with time ? > > Thanks, > Mohamed > > On Wed, May 6, 2020 at 08:23 David van der Spoel > wrote: > > > Den 2020-05-06 kl. 01:13, skrev Mohamed Abdelaal: > > > Hello everybody, > > > > > > I have two fundamental questions please. > > > > > > I have measured the fee volume and I discovered that, the free volume > > > changes with respect to the time during the production run (different > > value > > > for each frame). However I have measured the density but the result > does > > > not change with respect to time. > > > > > > Shouldn't the density also changes with time if the free volume changes > > > with time ? > > > > > > I also can't understand why the free volume changes with respect to the > > > time, if the number of molecules and volume of box didn't change. > > > > > > Many Thanks, > > > Mohamed > > > > > This is due to atomic fluctuations, that is they overlap more or less > > depending on their distance, Did you use the freevolume tool in gromacs? > > It may also depend on whether each freevolume calculations is converged > > (-ninsert option). > > > > -- > > David van der Spoel, Ph.D., > > Professor of Biology > > Uppsala University. > > http://virtualchemistry.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] Free volume variation during the simulation
Are you simulating a crystal or amorphous system? Arun On Wed, May 6, 2020 at 12:13 AM Mohamed Abdelaal wrote: > Hello everybody, > > I have two fundamental questions please. > > I have measured the fee volume and I discovered that, the free volume > changes with respect to the time during the production run (different value > for each frame). However I have measured the density but the result does > not change with respect to time. > > Shouldn't the density also changes with time if the free volume changes > with time ? > > I also can't understand why the free volume changes with respect to the > time, if the number of molecules and volume of box didn't change. > > Many Thanks, > Mohamed > -- > 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] Question about Mean Square Displacement (MSD)
Unless you give you give details how you calculate the MSD it will not be possible to help. Are you using unwrapped co-ordinates in your calculations for MSD? Arun On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani wrote: > Hi, > I am trying to post-processing my results and calculate MSD (mean square > displacement) but my answer is different from the MSD value that GROMACS > calculated. I use trjconv command and use the output .gro file. I tried to > understand the GROMACS code but I am not a good programmer. Is there any > specific detail except the Einstein relation in the manual? > > sorry if here is not the right place to ask this question. > Best regards. > > Sina Omrani. > -- > 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] rdf coordination number over time (ns)
Hi if you have rdf it is easy to calculate the coordination number by numerical integration https://en.wikibooks.org/wiki/Molecular_Simulation/Radial_Distribution_Functions Arun On Mon, Nov 26, 2018 at 11:38 AM Maria Luisa wrote: > Dear users, > I need to calculate rdf coordination number over time. I have a pdb > trajecory of 200 ns, from which I want to evaluate g(r) and CN of Na-Cl, > Na-O, Cl-O. My gromacs works with VMD, but I cannot do coordination number > in function of time! Can you help me? > > Maria Luisa > > > Maria Luisa Perrotta > Ph.D Student, CNR-ITM > via P.Bucci, 87036 Rende (Cs) > Italy > email: ml.perro...@itm.cnr.it > > > -- > 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] Test particle insertion change in energy - group cut off scheme
I see. Thank you. I understand how tpi in gromacs works now. Perhaps my last question. Is there a restriction on the number of charge groups in gromacs ?. For example can it be equal to the number of atoms in the system ? How do think it will affect the performance of tpi which uses the group cut off scheme ? Thank you again Arun On Sat, Mar 3, 2018 at 9:44 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Please see the reference manual for details, but the charge groups are > defined in the topology however you wish (and need not have a net charge). > > Mark > > On Sun, Mar 4, 2018, 00:18 Arun Srikanth <askfora...@gmail.com> wrote: > > > Thank you. > > > > Can you please elaborate on this or clarify the following questions? > > > > 1. Supposing I have inserted one water molecule inside a polymer (an > > interconnected network with net zero charge), > > > > the electrostatic interactions should be computed between every atom of > > water and polymer atoms within a cutoff distance and use per atom > > ewald summation due to long-range nature of electrostatics. > > > > I believe if one chooses group cutoff the interactions are based on > centre > > of mass of charged groups ?. > > > > Also not clear how gromacs will handle charged group in this particular > > case since I have interconnected (crosslinked) network and not a fixed > > number of monomers in which case the all the atoms belonging to one > monomer > > can be considered a charged group. > > > > > > > > Thank you again > > Arun > > > > > > > > On Sat, Mar 3, 2018 at 5:44 PM, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > > > Hi, > > > > > > TPI will only work if you choose the group cutoff scheme. But the > impact > > of > > > that difference is nearly zero. > > > > > > Mark > > > > > > On Sat, Mar 3, 2018, 22:29 Arun Srikanth <askfora...@gmail.com> wrote: > > > > > > > Hello all > > > > > > > > I was going through tpi.cpp file in the latest version of gromacs. > > > > > > > > I found this flag > > > > > > > > "TPI does not work (yet) with the Verlet cut-off scheme" > > > > > > > > My question: > > > > > > > > Does test particle insertion use the group cut off scheme to > calculate > > > the > > > > change in energy ? (assuming equilibrium trajectories generated using > > > > verlet cutoff) > > > > > > > > Thank you > > > > Arun > > > > -- > > > > 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] Test particle insertion change in energy - group cut off scheme
Thank you. Can you please elaborate on this or clarify the following questions? 1. Supposing I have inserted one water molecule inside a polymer (an interconnected network with net zero charge), the electrostatic interactions should be computed between every atom of water and polymer atoms within a cutoff distance and use per atom ewald summation due to long-range nature of electrostatics. I believe if one chooses group cutoff the interactions are based on centre of mass of charged groups ?. Also not clear how gromacs will handle charged group in this particular case since I have interconnected (crosslinked) network and not a fixed number of monomers in which case the all the atoms belonging to one monomer can be considered a charged group. Thank you again Arun On Sat, Mar 3, 2018 at 5:44 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > TPI will only work if you choose the group cutoff scheme. But the impact of > that difference is nearly zero. > > Mark > > On Sat, Mar 3, 2018, 22:29 Arun Srikanth <askfora...@gmail.com> wrote: > > > Hello all > > > > I was going through tpi.cpp file in the latest version of gromacs. > > > > I found this flag > > > > "TPI does not work (yet) with the Verlet cut-off scheme" > > > > My question: > > > > Does test particle insertion use the group cut off scheme to calculate > the > > change in energy ? (assuming equilibrium trajectories generated using > > verlet cutoff) > > > > Thank you > > Arun > > -- > > 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] Test particle insertion change in energy - group cut off scheme
Hello all I was going through tpi.cpp file in the latest version of gromacs. I found this flag "TPI does not work (yet) with the Verlet cut-off scheme" My question: Does test particle insertion use the group cut off scheme to calculate the change in energy ? (assuming equilibrium trajectories generated using verlet cutoff) Thank you Arun -- 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] Two questions: LAMMPS to gromacs, Test particle insertion
Hello all, I have two questions. 1. Is there a tool to convert LAMMPS data file to gromacs topology file. I am using GAFF forcefield. Test particle insertion: In the manual it is mentioned that "This trajectory should not contain the molecule to be inserted." If I want to estimate excess chemical potential in a system with 2 wt% water, how should we do it since the trajectory would contain water. Any help is appreciated. Thank you Arun -- 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.
