[gmx-users] Drude force field
Dear users, How or where can I get the Drude polarizable force field file for current Gromacs version? -- 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] Keep having to path gromacs when opening a new terminal
If you have .bashrc file then just add this line in your .bashrc file then type source .bashrc vi .bashrc *source /usr/local/gromacs/bin/GMXRC* *source .bashrc* ** *Krishna Prasad Ghanta* *Research Scholar* *Molecular Modeling Laboratory* *Indian Institute Of Technology Kharagpur* *Kharagpur-721302Contact no - 8327297650* *** On Tue, 16 Jul 2019 at 22:15, Israel Estrada wrote: > Hello Users, > > I've compiled GROMACS successfully on my machine, but the gmx_mpi command > is not recognized until I enter the command > > source /usr/local/gromacs/bin/GMXRC > > everything works fine after, but is there a way I can avoid having to > enter that command every time I begin a new session? > > any help is appreciated, thank you! > -Israel > > -- > 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] Specific heat calculations using gmx energy
Thanks, Prof. Spoel. The Enthalpy does make a sudden drop and excluding that part, the heat capacity values does not differ much with time. However the values still are far from experimental values ( 7934.66 J/mol K* compared to ~ 100 *J/mol K). I am using 5.1.1 version, so I cant use the gmx dos program, it stop with an index error. I will try gmx dos in gromacs 2019 and check the Cp values again. On Wed, Jul 17, 2019 at 1:04 AM David van der Spoel wrote: > Den 2019-07-15 kl. 09:24, skrev Pragati Sharma: > > Dear all, > > > > I am simulating a melt of polybutadiene consisting of 60 chains using > OPLS > > forcefield. After 50 ns of NPT production run, specific heat is > calculated > > using the command: > > > > *gmx energy -f ener.edr -fluct_props -nmol 60 -driftcorr * > > and the value obtained is: > > Enthalpy =2010.04 kJ/mol > > Heat capacity at constant pressure *Cp=22807.5 J/mol K* > > > > However when I calculate Cp from last 5 ns of trajectory the value is: > > Enthalpy =2004.05 kJ/mol > > Heat capacity at constant pressure *Cp=7934.66 J/mol K* > > > > Do the Cp calculation is highly dependent on the equilibration of system > or > > I am missing something because the experimental valu is ~ 100 *J/mol K, > *so > > the values from simulation are also high compared to experiments. > > > > *Thanks* > > > Did you check whether the enthalpy makes a sudden drop in the beginning > of the simulation? If so this will influence the fluctuations a lot. > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > 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] Keep having to path gromacs when opening a new terminal
cd /etc/profile.d sudo ln -s /usr/local/gromacs/bin/GMXRC GMXRC.sh On 7/16/2019 8:14 PM, Israel Estrada wrote: Hello Users, I've compiled GROMACS successfully on my machine, but the gmx_mpi command is not recognized until I enter the command source /usr/local/gromacs/bin/GMXRC everything works fine after, but is there a way I can avoid having to enter that command every time I begin a new session? any help is appreciated, thank you! -Israel -- 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] Keep having to path gromacs when opening a new terminal
Hello Users, I've compiled GROMACS successfully on my machine, but the gmx_mpi command is not recognized until I enter the command source /usr/local/gromacs/bin/GMXRC everything works fine after, but is there a way I can avoid having to enter that command every time I begin a new session? any help is appreciated, thank you! -Israel -- 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] About g_sdf in version 4.6.5.
That is correct. (whoever is Darren? ;) ) 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 Tue, 16 Jul 2019 at 16:32, Henry Vider wrote: > Darren, so generating SDF over several molecules is possible with the > version you mentioned? > > Sincerely, > Henry > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Dallas > Warren > Sent: Tuesday, July 16, 2019 12:30:19 AM > To: GROMACS users > Subject: Re: [gmx-users] About g_sdf in version 4.6.5. > > Yes, it is still only summing over a single molecule since version 5 I > think, don't know exactly when the change occurred. Last version I have > used (and still use) for generating SDFs is 4.0.7 > > 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 Tue, 16 Jul 2019 at 01:43, Henry Vider wrote: > > > Dear all, > > > > I have a system consisting of 10 solute molecules and two different > > solvents. When generating Radial Distribution Functions and selecting the > > solute molecule for reference, I get RDFs averaged over 10 solute > > molecules. However, when generating SDF .cube file, results cannot be > > properly visualized in VMD for some reason. This is not the issue when I > > have systems consisting of 1 solute molecule and generate .cube files for > > these systems. > > > > I read in mailing list archives that SDF function does not average over > > several reference particles after version 3.x something. Is this still > true > > with even newer versions, and also in 4.6.5? > > > > Sincerely > > Henry > > -- > > 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] Specific heat calculations using gmx energy
Den 2019-07-15 kl. 09:24, skrev Pragati Sharma: Dear all, I am simulating a melt of polybutadiene consisting of 60 chains using OPLS forcefield. After 50 ns of NPT production run, specific heat is calculated using the command: *gmx energy -f ener.edr -fluct_props -nmol 60 -driftcorr * and the value obtained is: Enthalpy =2010.04 kJ/mol Heat capacity at constant pressure *Cp=22807.5 J/mol K* However when I calculate Cp from last 5 ns of trajectory the value is: Enthalpy =2004.05 kJ/mol Heat capacity at constant pressure *Cp=7934.66 J/mol K* Do the Cp calculation is highly dependent on the equilibration of system or I am missing something because the experimental valu is ~ 100 *J/mol K, *so the values from simulation are also high compared to experiments. *Thanks* Did you check whether the enthalpy makes a sudden drop in the beginning of the simulation? If so this will influence the fluctuations a lot. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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] heat capacity collection
Den 2019-07-16 kl. 13:30, skrev Amin Rouy: Hi everyone, I try to collect the heat capacities from my set of simulations. I see that the heat capacity through gmx energy -fluct_props does not provide an output file with the heat capacities. Any suggestion how can I collect them (or how to do with an script)? thanks What kind of systems are these? I have quite a few reference data for liquids on http://virtualchemistry.org These were done using the gmx dos program that computes quantum corrections but this is not entirely trivial. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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] Flat-bottomed Restrain
Ehsan, That is just a single cylinder, or if you wish you can call it 5 identical overlapping cylinders corresponding to each atom, but that still is just one cylinder. Actually you still have your original *.GRO of your system fed to grompp by -c flag, the reference.gro edited that way is just a reference coordinate by which you dictate the desired molecule to move around the axes at (3.0, 3,0) as much as 1.5 nm while the molecule is free to move along the Z as much as it likes. Regards, Salman Zarrini On Tue, Jul 16, 2019 at 1:03 PM ehsan shahini wrote: > Dear Salman, > > Thanks for the reply. For the first part, you are defining 5 cylinders with > a radius of 1.5. And, I'm not sure about your suggestion for editing the > .gro file in that particular manner since there is another option (function > 3,4,5) for restraining atoms in a layer. But you are changing the x and y > coordinates of the atoms. > > On Tue, 16 Jul 2019 at 19:36, Salman Zarrini > wrote: > > > Hi Ehsan, > > > > Here is how I understood and would implement the flat-bottom potential; > > > > Just suppose you intend to confine a molecule with five atoms in a > cylinder > > with radius of *\rho = 1.500* nm and axes positioned at *x = 3.000 and y > = > > 3.000 nm* parallel to the Z. > > First you need a posre.rho.itp in which the restrain's properties are > > defined; > > posre.rho.itp > > ;Z - Cylinder: > > [ position_restraints ] > > ; i funct g_z\rho(nm) K(kJ mol-1 nm-2) > > 1 2 8 *1.500* 3500 > > 2 2 8 *1.500* 3500 > > 3 2 8 *1.500* 3500 > > 4 2 8 *1.500* 3500 > > 5 2 8 *1.500* 3500 > > > > Similar to all other restrains the posre.rho.itp should come in the end > of > > [moleculetype] section of the desired molecule, for instance using #ifdef > > ... #endif to be called later in mdp file. > > > > You still need one more file to be fed to grompp using -r as reference > > positions, as Mark pointed out; > > ;reference.gro > > Reference > > *127972* > >1AMNA H14*1* *3.000 3.000* 4.325 ;(no confinement along > > the Z) > >1AMNA C11*2* *3.000 3.000* 3.789 > >1AMNA H12*3* *3.000 3.000* 2.405 > >1AMNA H13*4* *3.000 3.000* 5.608 > >1AMNA C10*5* *3.000 3.000* 4.390 > >... (rest of the unrestrained atoms) > >... (rest of the unrestrained atoms) > >... (rest of the unrestrained atoms) > >... (rest of the unrestrained atoms) > > > > I hope it works! > > > > Cheers, > > Salman Zarrini > > > > > > On Tue, Jul 16, 2019 at 4:58 AM Mark Abraham > > wrote: > > > > > Hi, > > > > > > On Tue., 16 Jul. 2019, 10:32 ehsan shahini, > > > wrote: > > > > > > > Dear all, > > > > > > > > 1. I need to restrain a small molecule in a region (cylindrical) and > I > > > want > > > > to restrain all of its atoms in that region. The best tool is > > > flat-bottomed > > > > restrain but it only restrains individual atoms in their > corresponding > > > > regions and not all the atoms in a single region. > > > > > > > > Hence, if I want to change the main code related to flat-bottomed > where > > > can > > > > I find it? > > > > > > > > > > No need. Use grompp -r to restrain the position of each atom to the > same > > > position that is the centre of the desired region. > > > > > > Another question > > > > > > > > 2. Can we introduce virtual sites in Gromacs which are static and > > defined > > > > by the user via the XYZ coordinates of them? > > > > > > > > > > No, but you can have frozen particles that have whatever interactions > > that > > > you choose. > > > > > > Mark > > > > > > > > > Kind regards, > > > > > > > > Ehsan > > > > -- > > > > 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
Re: [gmx-users] Flat-bottomed Restrain
Hi, He's set the reference positions (in the -r file), rather than changing the initial positions (with the -c file). Mark On Tue., 16 Jul. 2019, 19:03 ehsan shahini, wrote: > Dear Salman, > > Thanks for the reply. For the first part, you are defining 5 cylinders with > a radius of 1.5. And, I'm not sure about your suggestion for editing the > .gro file in that particular manner since there is another option (function > 3,4,5) for restraining atoms in a layer. But you are changing the x and y > coordinates of the atoms. > > On Tue, 16 Jul 2019 at 19:36, Salman Zarrini > wrote: > > > Hi Ehsan, > > > > Here is how I understood and would implement the flat-bottom potential; > > > > Just suppose you intend to confine a molecule with five atoms in a > cylinder > > with radius of *\rho = 1.500* nm and axes positioned at *x = 3.000 and y > = > > 3.000 nm* parallel to the Z. > > First you need a posre.rho.itp in which the restrain's properties are > > defined; > > posre.rho.itp > > ;Z - Cylinder: > > [ position_restraints ] > > ; i funct g_z\rho(nm) K(kJ mol-1 nm-2) > > 1 2 8 *1.500* 3500 > > 2 2 8 *1.500* 3500 > > 3 2 8 *1.500* 3500 > > 4 2 8 *1.500* 3500 > > 5 2 8 *1.500* 3500 > > > > Similar to all other restrains the posre.rho.itp should come in the end > of > > [moleculetype] section of the desired molecule, for instance using #ifdef > > ... #endif to be called later in mdp file. > > > > You still need one more file to be fed to grompp using -r as reference > > positions, as Mark pointed out; > > ;reference.gro > > Reference > > *127972* > >1AMNA H14*1* *3.000 3.000* 4.325 ;(no confinement along > > the Z) > >1AMNA C11*2* *3.000 3.000* 3.789 > >1AMNA H12*3* *3.000 3.000* 2.405 > >1AMNA H13*4* *3.000 3.000* 5.608 > >1AMNA C10*5* *3.000 3.000* 4.390 > >... (rest of the unrestrained atoms) > >... (rest of the unrestrained atoms) > >... (rest of the unrestrained atoms) > >... (rest of the unrestrained atoms) > > > > I hope it works! > > > > Cheers, > > Salman Zarrini > > > > > > On Tue, Jul 16, 2019 at 4:58 AM Mark Abraham > > wrote: > > > > > Hi, > > > > > > On Tue., 16 Jul. 2019, 10:32 ehsan shahini, > > > wrote: > > > > > > > Dear all, > > > > > > > > 1. I need to restrain a small molecule in a region (cylindrical) and > I > > > want > > > > to restrain all of its atoms in that region. The best tool is > > > flat-bottomed > > > > restrain but it only restrains individual atoms in their > corresponding > > > > regions and not all the atoms in a single region. > > > > > > > > Hence, if I want to change the main code related to flat-bottomed > where > > > can > > > > I find it? > > > > > > > > > > No need. Use grompp -r to restrain the position of each atom to the > same > > > position that is the centre of the desired region. > > > > > > Another question > > > > > > > > 2. Can we introduce virtual sites in Gromacs which are static and > > defined > > > > by the user via the XYZ coordinates of them? > > > > > > > > > > No, but you can have frozen particles that have whatever interactions > > that > > > you choose. > > > > > > Mark > > > > > > > > > Kind regards, > > > > > > > > Ehsan > > > > -- > > > > 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
Re: [gmx-users] Xeon Gold + RTX 5000
That is excellent information, thank you. None of us have dealt with AMD CPUs in a while, so would the combination of a Ryzen 3900X and two Quadro 2080 Ti be a good choice? Again, thanks! Alex On 7/16/2019 8:41 AM, Szilárd Páll wrote: Hi Alex, On Mon, Jul 15, 2019 at 8:53 PM Alex wrote: Hi all and especially Szilard! My glorious management asked me to post this here. One of our group members, an ex-NAMD guy, wants to use Gromacs for biophysics and the following basics have been spec'ed for him: CPU: Xeon Gold 6244 GPU: RTX 5000 or 6000 I'll be surprised if he runs systems with more than 50K particles. Could you please comment on whether this is a cost-efficient and reasonably powerful setup? Your past suggestions have been invaluable for us. That will be reasonably fast, but cost efficiency will be awful, to be honest: - that CPU is a ~$3000 part and won't perform much better than a $4-500 desktop CPU like an i9 9900, let alone a Ryzen 3900X which would be significantly faster. - Quadro cards also pretty low in bang for buck: a 2080 Ti will be close to the RTX 6000 for ~5x less and the 2080 or 2070 Super a bit slower for at least another 1.5x less. Single run at a time or possibly multiple? The proposed (or any 8+ core) workstation CPU is fast enough in the majority of the simulations to pair well with two of those GPUs if used for two concurrent simulations. If that's a relevant use-case, I'd recommend two 2070 Super or 2080 cards. Cheers, -- Szilárd 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. -- 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] Flat-bottomed Restrain
Dear Salman, Thanks for the reply. For the first part, you are defining 5 cylinders with a radius of 1.5. And, I'm not sure about your suggestion for editing the .gro file in that particular manner since there is another option (function 3,4,5) for restraining atoms in a layer. But you are changing the x and y coordinates of the atoms. On Tue, 16 Jul 2019 at 19:36, Salman Zarrini wrote: > Hi Ehsan, > > Here is how I understood and would implement the flat-bottom potential; > > Just suppose you intend to confine a molecule with five atoms in a cylinder > with radius of *\rho = 1.500* nm and axes positioned at *x = 3.000 and y = > 3.000 nm* parallel to the Z. > First you need a posre.rho.itp in which the restrain's properties are > defined; > posre.rho.itp > ;Z - Cylinder: > [ position_restraints ] > ; i funct g_z\rho(nm) K(kJ mol-1 nm-2) > 1 2 8 *1.500* 3500 > 2 2 8 *1.500* 3500 > 3 2 8 *1.500* 3500 > 4 2 8 *1.500* 3500 > 5 2 8 *1.500* 3500 > > Similar to all other restrains the posre.rho.itp should come in the end of > [moleculetype] section of the desired molecule, for instance using #ifdef > ... #endif to be called later in mdp file. > > You still need one more file to be fed to grompp using -r as reference > positions, as Mark pointed out; > ;reference.gro > Reference > *127972* >1AMNA H14*1* *3.000 3.000* 4.325 ;(no confinement along > the Z) >1AMNA C11*2* *3.000 3.000* 3.789 >1AMNA H12*3* *3.000 3.000* 2.405 >1AMNA H13*4* *3.000 3.000* 5.608 >1AMNA C10*5* *3.000 3.000* 4.390 >... (rest of the unrestrained atoms) >... (rest of the unrestrained atoms) >... (rest of the unrestrained atoms) >... (rest of the unrestrained atoms) > > I hope it works! > > Cheers, > Salman Zarrini > > > On Tue, Jul 16, 2019 at 4:58 AM Mark Abraham > wrote: > > > Hi, > > > > On Tue., 16 Jul. 2019, 10:32 ehsan shahini, > > wrote: > > > > > Dear all, > > > > > > 1. I need to restrain a small molecule in a region (cylindrical) and I > > want > > > to restrain all of its atoms in that region. The best tool is > > flat-bottomed > > > restrain but it only restrains individual atoms in their corresponding > > > regions and not all the atoms in a single region. > > > > > > Hence, if I want to change the main code related to flat-bottomed where > > can > > > I find it? > > > > > > > No need. Use grompp -r to restrain the position of each atom to the same > > position that is the centre of the desired region. > > > > Another question > > > > > > 2. Can we introduce virtual sites in Gromacs which are static and > defined > > > by the user via the XYZ coordinates of them? > > > > > > > No, but you can have frozen particles that have whatever interactions > that > > you choose. > > > > Mark > > > > > > Kind regards, > > > > > > Ehsan > > > -- > > > 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] Flat-bottomed Restrain
Hi Ehsan, Here is how I understood and would implement the flat-bottom potential; Just suppose you intend to confine a molecule with five atoms in a cylinder with radius of *\rho = 1.500* nm and axes positioned at *x = 3.000 and y = 3.000 nm* parallel to the Z. First you need a posre.rho.itp in which the restrain's properties are defined; posre.rho.itp ;Z - Cylinder: [ position_restraints ] ; i funct g_z\rho(nm) K(kJ mol-1 nm-2) 1 2 8 *1.500* 3500 2 2 8 *1.500* 3500 3 2 8 *1.500* 3500 4 2 8 *1.500* 3500 5 2 8 *1.500* 3500 Similar to all other restrains the posre.rho.itp should come in the end of [moleculetype] section of the desired molecule, for instance using #ifdef ... #endif to be called later in mdp file. You still need one more file to be fed to grompp using -r as reference positions, as Mark pointed out; ;reference.gro Reference *127972* 1AMNA H14*1* *3.000 3.000* 4.325 ;(no confinement along the Z) 1AMNA C11*2* *3.000 3.000* 3.789 1AMNA H12*3* *3.000 3.000* 2.405 1AMNA H13*4* *3.000 3.000* 5.608 1AMNA C10*5* *3.000 3.000* 4.390 ... (rest of the unrestrained atoms) ... (rest of the unrestrained atoms) ... (rest of the unrestrained atoms) ... (rest of the unrestrained atoms) I hope it works! Cheers, Salman Zarrini On Tue, Jul 16, 2019 at 4:58 AM Mark Abraham wrote: > Hi, > > On Tue., 16 Jul. 2019, 10:32 ehsan shahini, > wrote: > > > Dear all, > > > > 1. I need to restrain a small molecule in a region (cylindrical) and I > want > > to restrain all of its atoms in that region. The best tool is > flat-bottomed > > restrain but it only restrains individual atoms in their corresponding > > regions and not all the atoms in a single region. > > > > Hence, if I want to change the main code related to flat-bottomed where > can > > I find it? > > > > No need. Use grompp -r to restrain the position of each atom to the same > position that is the centre of the desired region. > > Another question > > > > 2. Can we introduce virtual sites in Gromacs which are static and defined > > by the user via the XYZ coordinates of them? > > > > No, but you can have frozen particles that have whatever interactions that > you choose. > > Mark > > > Kind regards, > > > > Ehsan > > -- > > 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] Flat-bottomed Restrain
Thank you so much for your response. For my first question, are you suggesting using a command like this: gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -r small_molecule.gro -o md.tpr This command, however, results in a warning and a fatal error: WARNING 1 [file unknown]: The number of atoms in small_molecule.gro (59) does not match the number of atoms in the topology (54073). Will assume that the first 59 atoms in the topology and small_molecule.gro match. fatal error: Can not invert matrix, determinant is zero Even though I changed the topology and npt.gro in a way that the first 59 atoms were the atoms of the small molecule the error insisted. Formerly, I used -r npt.gro and used flat-bottomed restrain on a single atom and it worked for that particle. So what does "-r" flag do? I read the manual but there is not much information on it. Kind regards, Ehsan On Tue, 16 Jul 2019 at 13:28, Mark Abraham wrote: > Hi, > > On Tue., 16 Jul. 2019, 10:32 ehsan shahini, > wrote: > > > Dear all, > > > > 1. I need to restrain a small molecule in a region (cylindrical) and I > want > > to restrain all of its atoms in that region. The best tool is > flat-bottomed > > restrain but it only restrains individual atoms in their corresponding > > regions and not all the atoms in a single region. > > > > Hence, if I want to change the main code related to flat-bottomed where > can > > I find it? > > > > No need. Use grompp -r to restrain the position of each atom to the same > position that is the centre of the desired region. > > Another question > > > > 2. Can we introduce virtual sites in Gromacs which are static and defined > > by the user via the XYZ coordinates of them? > > > > No, but you can have frozen particles that have whatever interactions that > you choose. > > Mark > > > Kind regards, > > > > Ehsan > > -- > > 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] Xeon Gold + RTX 5000
Hi Alex, On Mon, Jul 15, 2019 at 8:53 PM Alex wrote: > > Hi all and especially Szilard! > > My glorious management asked me to post this here. One of our group > members, an ex-NAMD guy, wants to use Gromacs for biophysics and the > following basics have been spec'ed for him: > > CPU: Xeon Gold 6244 > GPU: RTX 5000 or 6000 > > I'll be surprised if he runs systems with more than 50K particles. Could > you please comment on whether this is a cost-efficient and reasonably > powerful setup? Your past suggestions have been invaluable for us. That will be reasonably fast, but cost efficiency will be awful, to be honest: - that CPU is a ~$3000 part and won't perform much better than a $4-500 desktop CPU like an i9 9900, let alone a Ryzen 3900X which would be significantly faster. - Quadro cards also pretty low in bang for buck: a 2080 Ti will be close to the RTX 6000 for ~5x less and the 2080 or 2070 Super a bit slower for at least another 1.5x less. Single run at a time or possibly multiple? The proposed (or any 8+ core) workstation CPU is fast enough in the majority of the simulations to pair well with two of those GPUs if used for two concurrent simulations. If that's a relevant use-case, I'd recommend two 2070 Super or 2080 cards. Cheers, -- Szilárd > 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. -- 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] Hydrogen bond analysis
Hi allI want to carry on a hydrogen bond analysis between a protein and ligand. I tested hbond but it only gives the number of hydrogen bonds which I am not looking for. I want to know exactly which residues are involved in hydrogen bonding and more specifically which atoms of the residues and ligand have interaction during the whole simulation time.Any help would be appreciated!Thank you. -- 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] heat capacity collection
Hi everyone, I try to collect the heat capacities from my set of simulations. I see that the heat capacity through gmx energy -fluct_props does not provide an output file with the heat capacities. Any suggestion how can I collect them (or how to do with an script)? 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] Generating Ramachandran Plot monitoring movie.
Good Evening Friends, I had some problem with my MD analysis. I want to monitor the Ramachandran plot of some residues. My problem let say I had a tri peptide from which we can get 4 dihedral angles and we can only plot the ramachandran plot for the Mid residue that is second residue. Here What I want is some script or Method to monitor the changes occur in the Ramachandran plot during the simulation period. Let say I have 1000 saved frames each frame has it own Ramachandran plot I want like 40 sec or less duration movie or of the Ramachandran plot from frame 1 to 1000. Them I can monitor the the path in which the peptide secondary structures changes from the frame 1 to 1000. Thank You. -- 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] force constant (K_fb)
Hi, I would generally not bother. You're already modelling something unphysical. What is the consequence for your observations of either an unexpectedly large range of position, or an uncharacteristic distribution of KE? Mark On Mon., 15 Jul. 2019, 20:13 Alex, wrote: > Dear Gromacs user, > Using flat-bottom potential I am creating a cubic box (wall) to keep some > of the molecules in a specific region of the box. I wonder if it is matter > how large or small the force constant (k_fb) be as far as the created wall > does the job well? > For instance I just chose the 4184 (Kj mol-1 nm-2) for k_fb with no reason > and it works fine in my case, do you think I should check if any other > smaller k_fb works and use the smaller one? > > Regards, > 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. > -- 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] Flat-bottomed Restrain
Hi, On Tue., 16 Jul. 2019, 10:32 ehsan shahini, wrote: > Dear all, > > 1. I need to restrain a small molecule in a region (cylindrical) and I want > to restrain all of its atoms in that region. The best tool is flat-bottomed > restrain but it only restrains individual atoms in their corresponding > regions and not all the atoms in a single region. > > Hence, if I want to change the main code related to flat-bottomed where can > I find it? > No need. Use grompp -r to restrain the position of each atom to the same position that is the centre of the desired region. Another question > > 2. Can we introduce virtual sites in Gromacs which are static and defined > by the user via the XYZ coordinates of them? > No, but you can have frozen particles that have whatever interactions that you choose. Mark Kind regards, > > Ehsan > -- > 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] Flat-bottomed Restrain
Dear all, 1. I need to restrain a small molecule in a region (cylindrical) and I want to restrain all of its atoms in that region. The best tool is flat-bottomed restrain but it only restrains individual atoms in their corresponding regions and not all the atoms in a single region. Hence, if I want to change the main code related to flat-bottomed where can I find it? Another question 2. Can we introduce virtual sites in Gromacs which are static and defined by the user via the XYZ coordinates of them? Kind regards, Ehsan -- 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] About g_sdf in version 4.6.5.
Darren, so generating SDF over several molecules is possible with the version you mentioned? Sincerely, Henry From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Dallas Warren Sent: Tuesday, July 16, 2019 12:30:19 AM To: GROMACS users Subject: Re: [gmx-users] About g_sdf in version 4.6.5. Yes, it is still only summing over a single molecule since version 5 I think, don't know exactly when the change occurred. Last version I have used (and still use) for generating SDFs is 4.0.7 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 Tue, 16 Jul 2019 at 01:43, Henry Vider wrote: > Dear all, > > I have a system consisting of 10 solute molecules and two different > solvents. When generating Radial Distribution Functions and selecting the > solute molecule for reference, I get RDFs averaged over 10 solute > molecules. However, when generating SDF .cube file, results cannot be > properly visualized in VMD for some reason. This is not the issue when I > have systems consisting of 1 solute molecule and generate .cube files for > these systems. > > I read in mailing list archives that SDF function does not average over > several reference particles after version 3.x something. Is this still true > with even newer versions, and also in 4.6.5? > > Sincerely > Henry > -- > 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.
