Re: [gmx-users] Surface tension
Thank you Andre. Your explanation answers my question very well. On Tue, May 10, 2016 at 10:31 PM, André Farias de Moura <mo...@ufscar.br> wrote: > Hi Ganesh, > > as any other pressure-related property, surface tension values over narrow > timescales are really noisy for systems in the range of nanometers > (increasing area should reduce the fluctuation). > > If simulations last long enough, average values should be OK (please mind > that average values may be different from experimental values, unless your > force field has been parametrized to reproduce surface tension itself, > which is not the case for most force fields). > > I hope it helps > > Andre > > On Tue, May 10, 2016 at 3:14 PM, Ganesh Shahane <ganesh7shah...@gmail.com> > wrote: > > > Dear Gromacs Users, > > > > I have been trying to calculate the surface tension of pure water in a > > cubic box, in which a layer of water molecules (along the XY plane) is > > surrounded by vacuum on either sides of the Z-direction. Towards this, I > > did an NVT simulation and computed the surface tension using gmx energy > > (Gromacs 5.1) and got the following results:- > > > > 1000.00 891.987000 > > 1005.00 -1404.097290 > > 1010.00 946.841919 > > 1015.00 2523.864014 > > 1020.00 317.747986 > > 1025.00 422.096313 > > 1030.00 -1233.948364 > > 1035.00 2187.071777 > > 1040.00 -88.564178 > > 1045.00 -981.897888 > > 1050.00 -429.718262 > > 1055.00 121.672829 > > . > > . > > . > > . > > > > My question is are the figures obtained as above normal/correct? My > concern > > is mainly because of the wide fluctuations in these readings. Also, when > > you report the value of surface tension, do you average the numbers > across > > all the frames? > > > > Any help would be appreciated. > > > > Thank you! > > > > -- > > Cheers! > > Ganesh Shahane > > -- > > 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. > > > > > > -- > _ > > Prof. Dr. André Farias de Moura > Department of Chemistry > Federal University of São Carlos > São Carlos - Brazil > phone: +55-16-3351-8090 > -- > 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. -- Best Regards, Ganesh Shahane -- 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] Surface tension
Dear Gromacs Users, I have been trying to calculate the surface tension of pure water in a cubic box, in which a layer of water molecules (along the XY plane) is surrounded by vacuum on either sides of the Z-direction. Towards this, I did an NVT simulation and computed the surface tension using gmx energy (Gromacs 5.1) and got the following results:- 1000.00 891.987000 1005.00 -1404.097290 1010.00 946.841919 1015.00 2523.864014 1020.00 317.747986 1025.00 422.096313 1030.00 -1233.948364 1035.00 2187.071777 1040.00 -88.564178 1045.00 -981.897888 1050.00 -429.718262 1055.00 121.672829 . . . . My question is are the figures obtained as above normal/correct? My concern is mainly because of the wide fluctuations in these readings. Also, when you report the value of surface tension, do you average the numbers across all the frames? Any help would be appreciated. Thank you! -- Cheers! Ganesh Shahane -- 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] Topology for Sphingomyelin
Hi Justin, I have stumbled upon another problem. The sphingomyelin topology (PSM.itp) that Charmm-GUI provides has an atomtype called NHL that is not defined by the Charmm36 ff. I am using the latest charmm36-jun2015.ff. Could you please look in to this? On Fri, Jan 22, 2016 at 4:29 PM, Ganesh Shahane <ganesh7shah...@gmail.com> wrote: > Thank you for your reply Justin!. It was helpful. > > On Fri, Jan 22, 2016 at 2:41 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 1/22/16 8:51 AM, Ganesh Shahane wrote: >> >>> Dear Gromacs users, >>> >>> I wish to simulate a mixed lipid bilayer of which one of the lipids is >>> sphingomyelin (PSM, 18:1-sphingosine and 16:0-palmitic acid) using >>> Charmm36 >>> ff. Towards this, I constructed the bilayer using Charmm-GUI but then was >>> surprised to find that its topology is not present in residue topology >>> database of Charmm36 ff. >>> >>> Does anyone has any idea about where can I get topology for PSM? Or would >>> it be wise to submit it to paramchem to get its topology? >>> >>> >> Use the force field CHARMM-GUI provides you. It supports everything in >> your system. Our charmm36.ff port may not include everything; I extend it >> only when people ask for specific parameters (as CHARMM is a huge force >> field, sometimes things get missed and I rely on this kind of feedback). >> I'll add sphingomyelin in the next release. >> >> -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. >> > > > > -- > Best Regards, > Ganesh Shahane > -- Best Regards, Ganesh Shahane -- 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] Topology for Sphingomyelin
Dear Gromacs users, I wish to simulate a mixed lipid bilayer of which one of the lipids is sphingomyelin (PSM, 18:1-sphingosine and 16:0-palmitic acid) using Charmm36 ff. Towards this, I constructed the bilayer using Charmm-GUI but then was surprised to find that its topology is not present in residue topology database of Charmm36 ff. Does anyone has any idea about where can I get topology for PSM? Or would it be wise to submit it to paramchem to get its topology? Thank you in advance. -- Best Regards, Ganesh Shahane -- 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] Topology for Sphingomyelin
Thank you for your reply Justin!. It was helpful. On Fri, Jan 22, 2016 at 2:41 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/22/16 8:51 AM, Ganesh Shahane wrote: > >> Dear Gromacs users, >> >> I wish to simulate a mixed lipid bilayer of which one of the lipids is >> sphingomyelin (PSM, 18:1-sphingosine and 16:0-palmitic acid) using >> Charmm36 >> ff. Towards this, I constructed the bilayer using Charmm-GUI but then was >> surprised to find that its topology is not present in residue topology >> database of Charmm36 ff. >> >> Does anyone has any idea about where can I get topology for PSM? Or would >> it be wise to submit it to paramchem to get its topology? >> >> > Use the force field CHARMM-GUI provides you. It supports everything in > your system. Our charmm36.ff port may not include everything; I extend it > only when people ask for specific parameters (as CHARMM is a huge force > field, sometimes things get missed and I rely on this kind of feedback). > I'll add sphingomyelin in the next release. > > -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. > -- Best Regards, Ganesh Shahane -- 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] Simulations of inorganic polymers
Dear Gromacs Users, I need to simulate a specific polymer which consists of carbon, hydrogen and fluorine atoms. Could anyone please suggest some force fields for simulating inorganic polymer molecules that have been ported to gromacs? Thank you. -- Best Regards, Ganesh Shahane -- 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] Backmapping of POPE
Dear Gromacs users, I have a mixed POPE:POPG bilayer in Martini ff which I wish to backmap into Charmm36 ff. To that effect, I am using the script developed by Tsjerk. However, I am getting the following error, which terminates the process even before it starts: Problem determining mapping coordinates for atom H91 of residue POPE. On checking the pope.charmm36.map file in Mapping folder, the atom H91 can be seen to be well defined in the bead D3B. Can anybody explain as to why it's throwing the error? Thank you. -- Best Regards, Ganesh Shahane -- 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] POPC simulation with heavy hydrogens and 4 fs timestep
Dear Gromacs Users, I have been trying to simulate a pure POPC bilayer with a timestep of 4 fs and heavy hydrogens, using the charmm36 ff. Towards this end, I constructed the bilayer using Charmm-GUI and used pdb2gmx with the -heavyh flag to generate the appropriate topology. However when I use the grompp to generate the .tpr file, I get a warning: "Overriding atomtype OT". A quick look in the Charmm36 ffnonbonded.itp revealed that the atomtype OT corresponds to an oxygen with reduced atomic mass, which is perfectly understandable given the use of -heavyh flag. My problem is that I don't understand what the warning exactly means. A look at a previous gromacs thread where this "overriding atomtype" problem has been reported, didn't help. Is it safe to ignore this warning? When I ignored the warning and carried out a simple NVE run, it gave me potential, kinetic and total energies that were not conserved. Please find the plot of the energies and the associated NVE run parameters at this link https://drive.google.com/file/d/0B2cmuCsErAPZcjhmNW1tWnA3UXM/view?usp=sharing. A look at the trajectory in VMD revealed that the molecules which were initially very dynamic, start "freezing" as the KE approaches zero. Does anybody has any idea as to where I am going wrong? Thank you. -- Best Regards, Ganesh Shahane -- 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] trjconv -pbc nojump
Hi Reisser, Instead of using -pbc nojump, use -pbc whole. On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) < sabine.reis...@kit.edu> wrote: > Hi, > > > I want to use trjconv -pbc nojump to create a trajectory without box > jumping of molecules. The molecules (lipids) also start to diffuse out of > the box like they should, but in some a part of the molecule still jumps > (as I could observe in xy direction), while the rest doesn't, leading to > artificially long bonds in VMD. I tried trjconv -pbc nojump both with a tpr > file in the -s option, or a gro file (with only complete molecules), same > result. > > > I'd be glad if somebody could give me a hint. > > > Cheers > > Sabine > > > > -- > Dr. Sabine Reißer > Theoretical Chemical Biology > Institute of Physical Chemistry > Karlsruhe Institute of Technology > > -- > 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. > -- Best Regards, Ganesh Shahane -- 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] Few queries about microsecond long simulations
Hi Anu, Since .xtc doesn't store velocities, its a much more compact trajectory than it's .trr counterpart, i.e. it has a smaller size. Also, .xtc is more easier on your computer RAM than the .trr file, during visualizing or analyzing using the .xtc trajectories. If you are looking to save disk space and if you won't need the velocities, output only the xtc file. On Wed, Aug 19, 2015 at 2:57 PM, anu chandra anu80...@gmail.com wrote: Hi Felipe and Ganesh, Do we really need to save coordinates in both of these two formats - trr and .xtc?. If one save the .trr file, what is the need of .xtc file since .trr can provide all the informations required with higher precision. All I am looking for is to save some disk space. Thanks Anu On Tue, Aug 18, 2015 at 3:19 PM, anu chandra anu80...@gmail.com wrote: Many thanks for your suggestions. On Tue, Aug 18, 2015 at 12:52 PM, Ganesh Shahane ganesh7shah...@gmail.com wrote: Hi Anu, 1) It really depends on what kind of analysis you are doing. If you are, for example, studying bio-molecular interactions that take place over microsecond long timescales then saving trajectories every 200-500 ps is advisable. I myself do receptor-membrane atomistic simulations with a saving frequency of 500 ps. You don't really need saving which is as frequent as 10 ps. 2), 3) Whereas .xtc trajectories contain only the coordinates, .trr trajectories contain both coordinates as well as velocities. So unless you are going to do any analysis which involves the velocities of atoms/particles, its safe to not write-out the .trr file. Still you are never really sure if you are going to require velocities or not and so it's best to write out the .trr file as well. On Tue, Aug 18, 2015 at 4:30 PM, Felipe Merino felipe.mer...@mpi-dortmund.mpg.de wrote: Hi, This are all questions that mostly only you can answer. On 18/08/15 12:42, anu chandra wrote: Dear Gromcas users, I am planning to do microsecond long simulation of membrane-protein system and I have ~100,000 atoms in the systems. Since I am trying for microsecond long simulations and I have a quiet large system, it can generate large amount of data and in this regard I would like to clarify few queries before continue the simulations. My queries are, 1. How often I should save the trajectories? In general, I have seen that mostly use 2ps interval for saving trajectories, as shown below. Will it be safe if I use 10ps ( 5000 steps ) interval for saving trajectories? nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps The files you create and the frequency with which you write them depends only on what you want to measure in the end. In principle, you want to save every couple of decorrelation times, for whatever property interests you. I assume that since you want a microsecond-long simulation then you are going for a slow process and therefore you don't need so frequent saving. Just as a comparison, for one of my simulations (~550k atoms, 1 µs) I save the coordinates every 40 ps which gives me a final xtc of ~50Gb of space. 2. How safe if I just write only the compressed .xtc file of the trajectories and not the .trr file during the production run? If its safe, how can I tell mdrun not to write the trr file? 3. Do I really need the trr file for any MD analysis? Again, you should know if you need the velocities later, or if need a high precision for the coordinates. If you don't, then leave the mdp as, nstxout = 0 nstvout = 0 nstenergy = 1000 nstlog = 1000 nstxtcout = 1000 Many thanks in advance Anu -- Felipe Merino Max Planck Institute for Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund Phone: +49 231 133 2306 -- 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. -- Best Regards, Ganesh Shahane -- 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] Few queries about microsecond long simulations
Hi Anu, 1) It really depends on what kind of analysis you are doing. If you are, for example, studying bio-molecular interactions that take place over microsecond long timescales then saving trajectories every 200-500 ps is advisable. I myself do receptor-membrane atomistic simulations with a saving frequency of 500 ps. You don't really need saving which is as frequent as 10 ps. 2), 3) Whereas .xtc trajectories contain only the coordinates, .trr trajectories contain both coordinates as well as velocities. So unless you are going to do any analysis which involves the velocities of atoms/particles, its safe to not write-out the .trr file. Still you are never really sure if you are going to require velocities or not and so it's best to write out the .trr file as well. On Tue, Aug 18, 2015 at 4:30 PM, Felipe Merino felipe.mer...@mpi-dortmund.mpg.de wrote: Hi, This are all questions that mostly only you can answer. On 18/08/15 12:42, anu chandra wrote: Dear Gromcas users, I am planning to do microsecond long simulation of membrane-protein system and I have ~100,000 atoms in the systems. Since I am trying for microsecond long simulations and I have a quiet large system, it can generate large amount of data and in this regard I would like to clarify few queries before continue the simulations. My queries are, 1. How often I should save the trajectories? In general, I have seen that mostly use 2ps interval for saving trajectories, as shown below. Will it be safe if I use 10ps ( 5000 steps ) interval for saving trajectories? nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps The files you create and the frequency with which you write them depends only on what you want to measure in the end. In principle, you want to save every couple of decorrelation times, for whatever property interests you. I assume that since you want a microsecond-long simulation then you are going for a slow process and therefore you don't need so frequent saving. Just as a comparison, for one of my simulations (~550k atoms, 1 µs) I save the coordinates every 40 ps which gives me a final xtc of ~50Gb of space. 2. How safe if I just write only the compressed .xtc file of the trajectories and not the .trr file during the production run? If its safe, how can I tell mdrun not to write the trr file? 3. Do I really need the trr file for any MD analysis? Again, you should know if you need the velocities later, or if need a high precision for the coordinates. If you don't, then leave the mdp as, nstxout = 0 nstvout = 0 nstenergy = 1000 nstlog = 1000 nstxtcout = 1000 Many thanks in advance Anu -- Felipe Merino Max Planck Institute for Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund Phone: +49 231 133 2306 -- 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. -- Best Regards, Ganesh Shahane -- 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] Topology file for serotonin (5-HT)
Hi Justin, Yes. I tried the same, but during the preparation of the .tpr file using grompp it gives an error saying No default proper dihedral types for 3 dihedral angles which are not present in the ffbonded.itp of the charmm36 force-field. These 3 dihedrals consist of atoms that encompass the alkyl amine and the indole groups of serotonin. Now, if I remove these dihedrals in question from the serotonin's .itp file which I have prepared, the simulation runs just fine. I am trying to calculate the free energy of solvation for serotonin. Considering this, is it okay to ignore some of these dihedrals? Thanks! On Mon, Jul 27, 2015 at 5:43 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/23/15 2:10 AM, Ganesh Shahane wrote: Dear Gromacs Users, I am looking forward to performing some simulations of a receptor bound to serotonin (also known as 5-HT). Does anybody have the .itp file of serotonin for the charmm27 or charmm36 force field? Thank you! It's very straightforward to combine existing parameters to make this simple molecule (indole + hydroxyl + alkyl amine). CHARMM covers all of these functional groups easily. -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. -- Best Regards, Ganesh Shahane -- 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] Topology file for serotonin (5-HT)
Dear Gromacs Users, I am looking forward to performing some simulations of a receptor bound to serotonin (also known as 5-HT). Does anybody have the .itp file of serotonin for the charmm27 or charmm36 force field? Thank you! -- Best Regards, Ganesh Shahane -- 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] g_msd and Diffusion Constant
Yes, for some calculations the error bar values did exceed the diffusion coefficient values. I am using the double-precision version of gromacs. But then again the question is whether to consider the value displayed on the terminal screen or the one displayed in the .xvg file. On Tue, Jul 21, 2015 at 10:25 PM, V.V.Chaban vvcha...@gmail.com wrote: I have a strong belief that an error bar for such numbers exceed the diffusion coefficient values. Newer gromacs versions (or is it just because of a double-precision compilation?) output more digits. I do want to hope these digits are meaningful If I got this situation, I would report 10^(-8)cm^2/s. On Tue, Jul 21, 2015 at 2:14 AM, Ganesh Shahane ganesh7shah...@gmail.com wrote: Hi! I am using gromacs version 4.5.5. The values are different. The value displayed on the terminal screen is 0.0007417*1e-5 cm^2/s while the value displayed in the chol.xvg file is 0.000903331*1e-5 cm^2/s. As you can see, both values are quite close though the value in chol.xvg doesn't appear to be round up. On Tue, Jul 21, 2015 at 10:20 AM, Chandan Choudhury iitd...@gmail.com wrote: Hi!! Are the values different? Can you show us both the values? I presume both values would be same. The value in the xvg file would be round up. Chandan On Tue, Jul 21, 2015 at 1:33 AM, V.V.Chaban vvcha...@gmail.com wrote: which version fo you use? On Mon, Jul 20, 2015 at 8:28 AM, Ganesh Shahane ganesh7shah...@gmail.com wrote: Dear Gromacs Users, I have performed a simulation of a POPC+Cholesterol bilayer. I wish to know the diffusion constant of a particular cholesterol molecule. Towards this, I performed a g_msd using the command as follows- g_msd -f 30chol.xtc -s prod.tpr -lateral z -endfit 80 -n index.ndx -mol chol.xvg where index.ndx contains a single index for the cholesterol atoms in question. In the end, I got 2 different values of diffusion constant, with one of them being displayed on the terminal screen and the other value in the chol.xvg file. Does anyone have any idea as to which value should be taken as the value of diffusion constant? Any help would be appreciated. Thank you! -- Best Regards, Ganesh Shahane -- 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. -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India *All work and no play makes Jack a dull boy...”* -- 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. -- Best Regards, Ganesh Shahane -- 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. -- Best Regards, Ganesh Shahane -- 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] g_msd and Diffusion Constant
Hi, Actually you are right. The chol.xvg file shows a value of 0.000903331 and NOT 0.000903331*1e-5. I initially thought that the .xvg file purposely doesn't show the 1e-5 value. But still 0.000903331 is different from 0.0007417 which is displayed on the terminal screen. On Tue, Jul 21, 2015 at 11:18 AM, Chandan Choudhury iitd...@gmail.com wrote: Yeah. Generally, what my observation says that in xvg file you have the round up value which has 4 decimal digits. But for your one it has 10 decimal degits. Can you please try with a higher version- 4.6.x? On Tue, Jul 21, 2015 at 10:44 AM, Ganesh Shahane ganesh7shah...@gmail.com wrote: Hi! I am using gromacs version 4.5.5. The values are different. The value displayed on the terminal screen is 0.0007417*1e-5 cm^2/s while the value displayed in the chol.xvg file is 0.000903331*1e-5 cm^2/s. As you can see, both values are quite close though the value in chol.xvg doesn't appear to be round up. On Tue, Jul 21, 2015 at 10:20 AM, Chandan Choudhury iitd...@gmail.com wrote: Hi!! Are the values different? Can you show us both the values? I presume both values would be same. The value in the xvg file would be round up. Chandan On Tue, Jul 21, 2015 at 1:33 AM, V.V.Chaban vvcha...@gmail.com wrote: which version fo you use? On Mon, Jul 20, 2015 at 8:28 AM, Ganesh Shahane ganesh7shah...@gmail.com wrote: Dear Gromacs Users, I have performed a simulation of a POPC+Cholesterol bilayer. I wish to know the diffusion constant of a particular cholesterol molecule. Towards this, I performed a g_msd using the command as follows- g_msd -f 30chol.xtc -s prod.tpr -lateral z -endfit 80 -n index.ndx -mol chol.xvg where index.ndx contains a single index for the cholesterol atoms in question. In the end, I got 2 different values of diffusion constant, with one of them being displayed on the terminal screen and the other value in the chol.xvg file. Does anyone have any idea as to which value should be taken as the value of diffusion constant? Any help would be appreciated. Thank you! -- Best Regards, Ganesh Shahane -- 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. -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India *All work and no play makes Jack a dull boy...”* -- 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. -- Best Regards, Ganesh Shahane -- 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. -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India *All work and no play makes Jack a dull boy...”* -- 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. -- Best Regards, Ganesh Shahane -- 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] g_msd and Diffusion Constant
Dear Gromacs Users, I have performed a simulation of a POPC+Cholesterol bilayer. I wish to know the diffusion constant of a particular cholesterol molecule. Towards this, I performed a g_msd using the command as follows- g_msd -f 30chol.xtc -s prod.tpr -lateral z -endfit 80 -n index.ndx -mol chol.xvg where index.ndx contains a single index for the cholesterol atoms in question. In the end, I got 2 different values of diffusion constant, with one of them being displayed on the terminal screen and the other value in the chol.xvg file. Does anyone have any idea as to which value should be taken as the value of diffusion constant? Any help would be appreciated. Thank you! -- Best Regards, Ganesh Shahane -- 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] g_msd and Diffusion Constant
Hi! I am using gromacs version 4.5.5. The values are different. The value displayed on the terminal screen is 0.0007417*1e-5 cm^2/s while the value displayed in the chol.xvg file is 0.000903331*1e-5 cm^2/s. As you can see, both values are quite close though the value in chol.xvg doesn't appear to be round up. On Tue, Jul 21, 2015 at 10:20 AM, Chandan Choudhury iitd...@gmail.com wrote: Hi!! Are the values different? Can you show us both the values? I presume both values would be same. The value in the xvg file would be round up. Chandan On Tue, Jul 21, 2015 at 1:33 AM, V.V.Chaban vvcha...@gmail.com wrote: which version fo you use? On Mon, Jul 20, 2015 at 8:28 AM, Ganesh Shahane ganesh7shah...@gmail.com wrote: Dear Gromacs Users, I have performed a simulation of a POPC+Cholesterol bilayer. I wish to know the diffusion constant of a particular cholesterol molecule. Towards this, I performed a g_msd using the command as follows- g_msd -f 30chol.xtc -s prod.tpr -lateral z -endfit 80 -n index.ndx -mol chol.xvg where index.ndx contains a single index for the cholesterol atoms in question. In the end, I got 2 different values of diffusion constant, with one of them being displayed on the terminal screen and the other value in the chol.xvg file. Does anyone have any idea as to which value should be taken as the value of diffusion constant? Any help would be appreciated. Thank you! -- Best Regards, Ganesh Shahane -- 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. -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India *All work and no play makes Jack a dull boy...”* -- 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. -- Best Regards, Ganesh Shahane -- 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.
