[gmx-users] walls and E-z
Hi all, It appears that the external field is refusing to move the ions when walls are present. I am comparing two setups of a system that has an aqueous bath (1M KCl) split by a semi-porous (infinitely selective for cations) membrane in XY. The only difference between them is that one is periodic in XYZ and the other has two walls. The difference isn't minor -- consider K+ fluxes with and without walls: https://www.dropbox.com/s/jve0hqqpfkn4ui6/flux.jpg?dl=0 Initially, ionic populations in each case are homogeneous. I realize that with walls the process will stop when all cations end up at the top of the box (and that's the goal). However, there is no flux right from the start. Relevant portion of the mdp with walls below (not sure if this is important, but 'ewald-geometry' directive isn't in the mdp without walls): pbc = xy nwall = 2 wall-type = 12-6 wall-r-linpot = 0.25 wall_atomtype = opls_996 opls_996 wall-ewald-zfac = 3 periodic_molecules = yes ns_type = grid rlist = 1.0 coulombtype = pme ewald-geometry = 3dc fourierspacing = 0.135 rcoulomb= 1.0 rvdw= 1.0 vdwtype = cut-off cutoff-scheme = Verlet Any ideas? Thanks, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] reliability of PMF
Hi, I've been trying to study a protein-ligand PMF using umbrella sampling strategy. So far, I have obtained the PMF following the tutorial and after performing bootstrapping the error is estimated to be at most 0.4 kcal/mol. Now, given the error value can I comment about changes like 2-3 kcal/mol in PMF ? I mean, with this error rate, how precise I can consider my PMF curve ? Any comments and/or references would be highly appreciated. Thank you -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- 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] angle/distance/position restraints in alchemical free energy calculation
Dear gmx user, I’m studying about alchemical free energy calculation. I have been read some articles about restraints during free energy calculation, they referred the procedure in the article (http://pubs.acs.org/doi/pdf/10.1021/jp0217839). I tried to search mailing list, but still I couldn’t understand. The manual said “restraint-lambdas” option only handle dihedral restraints, and the pull code restraints How to apply angle/distance/position restraints with respect to lambda? Thanks in advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Lost particles while sorting
On 11/2/2017 7:18 PM, Mark Abraham wrote: Granted. There's a bajillion ways for a newcomer to any simulation type to shoot themselves in the foot. Where would be a good place for "with walls, set up your simulation cell so the initial positions of all the particles are on the correct side of the wall?" See, because I am very far from a newcomer here, it became almost immediately after I posted initially. But we do have many newcomers who appear to have treated walls as a bug to the point of taking it to redmine. Even your first reaction was to take it there. I see your point very well, and it's both true and funny (essentially "set up your system like you're not an idiot"), but maybe we could say that lost particles are often caused by lack of outer vacuum layer between the system and the walls prior to running things. Just a suggestion, because everything seems to be okay in my simulation. :) Well, except for... That combination is one of the very large number of things in GROMACS that I know very little about. But a new topic might get the interest of any who do know! ... for this combination. I will post as soon as I can confirm this weirdness. Thanks! 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.
Re: [gmx-users] Lost particles while sorting
Hi, On Fri, Nov 3, 2017 at 2:11 AM Alex wrote: > Hi Mark, > > It may be a good idea for you guys to document walls a bit better than > what we have right now. What was happening became clear to me pretty > quickly, but the error text is kinda obscure and the documentation on > walls is brief. :) > Granted. There's a bajillion ways for a newcomer to any simulation type to shoot themselves in the foot. Where would be a good place for "with walls, set up your simulation cell so the initial positions of all the particles are on the correct side of the wall?" I am encountering more unexpected things with walls, e.g. rather strong > E-z not having any effect on ions -- still preliminary though. I suppose > this will probably need another thread if I confirm it, but do you have > any recollection of anything specific to walls + external fields? Yes, I > am indeed trying to separate the ionic population. ;) > That combination is one of the very large number of things in GROMACS that I know very little about. But a new topic might get the interest of any who do know! Mark Thanks, > > Alex > > > On 11/2/2017 6:11 PM, Mark Abraham wrote: > > Hi, > > > > Yes that seems consistent with some theories Berk had when we chatted > over > > lunch. Specifically, if the linear potential is too weak then you > wouldn't > > get the repulsion you seek. Clearly you've found some other more basic > ways > > that a system preparation protocol would not have respected the intended > > effect of that wall. > > > > BTW there is a "private" mode on Redmine that I hope normal users can use > > in cases where they have systems whose details they would like to keep > to a > > small group of need-to-know types. That will work better than getting > lost > > in my inbox. ;-) > > > > Mark > > > > On Thu, Nov 2, 2017 at 11:29 PM Alex wrote: > > > >> So, I have a bit of an update -- hopefully this will somewhat help > others > >> encountering this error, because it may not be entirely a bug... > >> > >> 1. The issue can be overcome by first and foremost not applying walls > to a > >> system previously run without any -- that was my mistake and it makes > >> physical sense. Dynamic equilibration has to be performed with walls and > >> corresponding pbc setting. This, however, does not guarantee anything if > >> the system is e.g. solvated -- that is, if there are atoms expected very > >> close to walls, or beyond them. In addition, if there atoms looking for > >> neighbors across the box (through previously set pbc), that can be > >> catastrophic. See below. > >> > >> 2. After solvating, but before EM, reinsert the system in a box slightly > >> larger in the z-direction. For a box initially 4 nm long in Z in my > case, > >> reinserting in a 4.6 nm long box worked here. > >> > >> 3. Particles seem to be lost when wall-r-linpot is set improperly, so > try > >> various values (0.25 nm worked for me). > >> > >> 4. The entire concept here is naturally very messy. I could think of > >> optional functionality, which allows for removing entire molecules whose > >> atoms are anticipated to be beyond walls, or close enough to result in > >> local explosions. However, that is also messy and can be done manually > in > >> previous steps, so no elegant suggestion from my end, unfortunately, > other > >> than being very mindful when setting this up. > >> > >> Alex > >> > >> > >> On Wed, Nov 1, 2017 at 6:26 PM, Alex wrote: > >> > >>> Mark, > >>> > >>> Could you please share your email address, so I can send you the tpr > >>> privately? I don't want this work to be public just yet, if that's > okay. > >>> > >>> Thanks, > >>> > >>> Alex > >>> > >>> > >>> On 11/1/2017 4:42 PM, Mark Abraham wrote: > >>> > Hi, > > We have had several reports of "lost particles while sorting" but we > >> would > like a .tpr on an issue on redmine.gromacs.org to be able to > >> investigate, > please! > > Mark > > On Wed, Nov 1, 2017 at 10:19 PM Alex wrote: > > Hi all, > > I am using walls in the cowboy mode, GMX v. 2016.3, system is a > porous > > membrane (periodic in XY) with water and ions -- everything works > fine > > with > > pbc=xyz and no walls. With walls, mdrun throws "Software > inconsistency > > error: Lost particles while sorting." > > > > mdp exerpt below: > > > > pbc = xy > > nwall = 2 > > wall-type = 12-6 > > wall-r-linpot = 0.0 > > wall_atomtype = opls_996 opls_996 > > wall-ewald-zfac = 3 > > periodic_molecules = yes > > ns_type = grid > > rlist = 1.0 > > coulombtype = pme > > ewald-geometry = 3dc > > fourierspacing = 0.135 > > rcoulomb= 1.0 > > rvdw= 1.0 > > vdwtype = cut-off > > cutoff-scheme = Verlet > > > > This uses a custom type "opls_996" properl
Re: [gmx-users] Lost particles while sorting
Hi Mark, It may be a good idea for you guys to document walls a bit better than what we have right now. What was happening became clear to me pretty quickly, but the error text is kinda obscure and the documentation on walls is brief. :) I am encountering more unexpected things with walls, e.g. rather strong E-z not having any effect on ions -- still preliminary though. I suppose this will probably need another thread if I confirm it, but do you have any recollection of anything specific to walls + external fields? Yes, I am indeed trying to separate the ionic population. ;) Thanks, Alex On 11/2/2017 6:11 PM, Mark Abraham wrote: Hi, Yes that seems consistent with some theories Berk had when we chatted over lunch. Specifically, if the linear potential is too weak then you wouldn't get the repulsion you seek. Clearly you've found some other more basic ways that a system preparation protocol would not have respected the intended effect of that wall. BTW there is a "private" mode on Redmine that I hope normal users can use in cases where they have systems whose details they would like to keep to a small group of need-to-know types. That will work better than getting lost in my inbox. ;-) Mark On Thu, Nov 2, 2017 at 11:29 PM Alex wrote: So, I have a bit of an update -- hopefully this will somewhat help others encountering this error, because it may not be entirely a bug... 1. The issue can be overcome by first and foremost not applying walls to a system previously run without any -- that was my mistake and it makes physical sense. Dynamic equilibration has to be performed with walls and corresponding pbc setting. This, however, does not guarantee anything if the system is e.g. solvated -- that is, if there are atoms expected very close to walls, or beyond them. In addition, if there atoms looking for neighbors across the box (through previously set pbc), that can be catastrophic. See below. 2. After solvating, but before EM, reinsert the system in a box slightly larger in the z-direction. For a box initially 4 nm long in Z in my case, reinserting in a 4.6 nm long box worked here. 3. Particles seem to be lost when wall-r-linpot is set improperly, so try various values (0.25 nm worked for me). 4. The entire concept here is naturally very messy. I could think of optional functionality, which allows for removing entire molecules whose atoms are anticipated to be beyond walls, or close enough to result in local explosions. However, that is also messy and can be done manually in previous steps, so no elegant suggestion from my end, unfortunately, other than being very mindful when setting this up. Alex On Wed, Nov 1, 2017 at 6:26 PM, Alex wrote: Mark, Could you please share your email address, so I can send you the tpr privately? I don't want this work to be public just yet, if that's okay. Thanks, Alex On 11/1/2017 4:42 PM, Mark Abraham wrote: Hi, We have had several reports of "lost particles while sorting" but we would like a .tpr on an issue on redmine.gromacs.org to be able to investigate, please! Mark On Wed, Nov 1, 2017 at 10:19 PM Alex wrote: Hi all, I am using walls in the cowboy mode, GMX v. 2016.3, system is a porous membrane (periodic in XY) with water and ions -- everything works fine with pbc=xyz and no walls. With walls, mdrun throws "Software inconsistency error: Lost particles while sorting." mdp exerpt below: pbc = xy nwall = 2 wall-type = 12-6 wall-r-linpot = 0.0 wall_atomtype = opls_996 opls_996 wall-ewald-zfac = 3 periodic_molecules = yes ns_type = grid rlist = 1.0 coulombtype = pme ewald-geometry = 3dc fourierspacing = 0.135 rcoulomb= 1.0 rvdw= 1.0 vdwtype = cut-off cutoff-scheme = Verlet This uses a custom type "opls_996" properly defined in ffnonbonded of the FF (custom OPLSAA). Any suggestions? I can provide more info, if needed. 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. -- 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 htt
Re: [gmx-users] short range electrostatic cutoff
Hi, No, there's nothing specific for that, other than user-tabulated interactions (currently only in the group scheme). But this wouldn't help you exclude the case of atoms coinciding. IIRC the Verlet short-ranged kernels have some slightly inefficient code that guards against that, but that wouldn't help you (yet). Mark On Thu, Nov 2, 2017 at 9:21 PM Adam Rettig wrote: > Hi all, > > I'm trying to find a way to prevent infinite attractive forces between > oppositely charged particles in my system using a purely coulombic > potential (without using a LJ potential). Does gromacs provide a way to > cutoff coulomb potential at short range, i.e. below a certain radius, the > coulombic potential stays constant instead of decreasing to negative > infinity? I can't seem to find any options that would do this. > > > Thanks, > Adam > -- > 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] Lost particles while sorting
Hi, Yes that seems consistent with some theories Berk had when we chatted over lunch. Specifically, if the linear potential is too weak then you wouldn't get the repulsion you seek. Clearly you've found some other more basic ways that a system preparation protocol would not have respected the intended effect of that wall. BTW there is a "private" mode on Redmine that I hope normal users can use in cases where they have systems whose details they would like to keep to a small group of need-to-know types. That will work better than getting lost in my inbox. ;-) Mark On Thu, Nov 2, 2017 at 11:29 PM Alex wrote: > So, I have a bit of an update -- hopefully this will somewhat help others > encountering this error, because it may not be entirely a bug... > > 1. The issue can be overcome by first and foremost not applying walls to a > system previously run without any -- that was my mistake and it makes > physical sense. Dynamic equilibration has to be performed with walls and > corresponding pbc setting. This, however, does not guarantee anything if > the system is e.g. solvated -- that is, if there are atoms expected very > close to walls, or beyond them. In addition, if there atoms looking for > neighbors across the box (through previously set pbc), that can be > catastrophic. See below. > > 2. After solvating, but before EM, reinsert the system in a box slightly > larger in the z-direction. For a box initially 4 nm long in Z in my case, > reinserting in a 4.6 nm long box worked here. > > 3. Particles seem to be lost when wall-r-linpot is set improperly, so try > various values (0.25 nm worked for me). > > 4. The entire concept here is naturally very messy. I could think of > optional functionality, which allows for removing entire molecules whose > atoms are anticipated to be beyond walls, or close enough to result in > local explosions. However, that is also messy and can be done manually in > previous steps, so no elegant suggestion from my end, unfortunately, other > than being very mindful when setting this up. > > Alex > > > On Wed, Nov 1, 2017 at 6:26 PM, Alex wrote: > > > Mark, > > > > Could you please share your email address, so I can send you the tpr > > privately? I don't want this work to be public just yet, if that's okay. > > > > Thanks, > > > > Alex > > > > > > On 11/1/2017 4:42 PM, Mark Abraham wrote: > > > >> Hi, > >> > >> We have had several reports of "lost particles while sorting" but we > would > >> like a .tpr on an issue on redmine.gromacs.org to be able to > investigate, > >> please! > >> > >> Mark > >> > >> On Wed, Nov 1, 2017 at 10:19 PM Alex wrote: > >> > >> Hi all, > >>> > >>> I am using walls in the cowboy mode, GMX v. 2016.3, system is a porous > >>> membrane (periodic in XY) with water and ions -- everything works fine > >>> with > >>> pbc=xyz and no walls. With walls, mdrun throws "Software inconsistency > >>> error: Lost particles while sorting." > >>> > >>> mdp exerpt below: > >>> > >>> pbc = xy > >>> nwall = 2 > >>> wall-type = 12-6 > >>> wall-r-linpot = 0.0 > >>> wall_atomtype = opls_996 opls_996 > >>> wall-ewald-zfac = 3 > >>> periodic_molecules = yes > >>> ns_type = grid > >>> rlist = 1.0 > >>> coulombtype = pme > >>> ewald-geometry = 3dc > >>> fourierspacing = 0.135 > >>> rcoulomb= 1.0 > >>> rvdw= 1.0 > >>> vdwtype = cut-off > >>> cutoff-scheme = Verlet > >>> > >>> This uses a custom type "opls_996" properly defined in ffnonbonded of > the > >>> FF (custom OPLSAA). Any suggestions? I can provide more info, if > needed. > >>> > >>> 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. > -- 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] Lost particles while sorting
So, I have a bit of an update -- hopefully this will somewhat help others encountering this error, because it may not be entirely a bug... 1. The issue can be overcome by first and foremost not applying walls to a system previously run without any -- that was my mistake and it makes physical sense. Dynamic equilibration has to be performed with walls and corresponding pbc setting. This, however, does not guarantee anything if the system is e.g. solvated -- that is, if there are atoms expected very close to walls, or beyond them. In addition, if there atoms looking for neighbors across the box (through previously set pbc), that can be catastrophic. See below. 2. After solvating, but before EM, reinsert the system in a box slightly larger in the z-direction. For a box initially 4 nm long in Z in my case, reinserting in a 4.6 nm long box worked here. 3. Particles seem to be lost when wall-r-linpot is set improperly, so try various values (0.25 nm worked for me). 4. The entire concept here is naturally very messy. I could think of optional functionality, which allows for removing entire molecules whose atoms are anticipated to be beyond walls, or close enough to result in local explosions. However, that is also messy and can be done manually in previous steps, so no elegant suggestion from my end, unfortunately, other than being very mindful when setting this up. Alex On Wed, Nov 1, 2017 at 6:26 PM, Alex wrote: > Mark, > > Could you please share your email address, so I can send you the tpr > privately? I don't want this work to be public just yet, if that's okay. > > Thanks, > > Alex > > > On 11/1/2017 4:42 PM, Mark Abraham wrote: > >> Hi, >> >> We have had several reports of "lost particles while sorting" but we would >> like a .tpr on an issue on redmine.gromacs.org to be able to investigate, >> please! >> >> Mark >> >> On Wed, Nov 1, 2017 at 10:19 PM Alex wrote: >> >> Hi all, >>> >>> I am using walls in the cowboy mode, GMX v. 2016.3, system is a porous >>> membrane (periodic in XY) with water and ions -- everything works fine >>> with >>> pbc=xyz and no walls. With walls, mdrun throws "Software inconsistency >>> error: Lost particles while sorting." >>> >>> mdp exerpt below: >>> >>> pbc = xy >>> nwall = 2 >>> wall-type = 12-6 >>> wall-r-linpot = 0.0 >>> wall_atomtype = opls_996 opls_996 >>> wall-ewald-zfac = 3 >>> periodic_molecules = yes >>> ns_type = grid >>> rlist = 1.0 >>> coulombtype = pme >>> ewald-geometry = 3dc >>> fourierspacing = 0.135 >>> rcoulomb= 1.0 >>> rvdw= 1.0 >>> vdwtype = cut-off >>> cutoff-scheme = Verlet >>> >>> This uses a custom type "opls_996" properly defined in ffnonbonded of the >>> FF (custom OPLSAA). Any suggestions? I can provide more info, if needed. >>> >>> 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] osmolytes box generation in gromacs
Dear all, I want to make 3M glycine box of size 6,6,6 in gromacs.can anyone tell me how to find the number of glycine molecule required for making 3M glycine box. Thanks in advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Cut-off radius larger than the box length for Deform option?
Dear Gromacs users, Why simulation doesn't crash when one of the box length gets smaller than the 2*cut-off radius mentioned in the MDP file, while using the deform option of Gromacs? I assume that there is some special provision for cut-off with deform option. I tried looking into the source code, and found the *deform* function in *mdlib/update.cpp*, however, I could not understand the code. Can someone please explain me how deform option works along with the cut-off, which makes the simulation to not crash. Thanks. Surya Prakash Tiwari -- 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] short range electrostatic cutoff
Hi all, I'm trying to find a way to prevent infinite attractive forces between oppositely charged particles in my system using a purely coulombic potential (without using a LJ potential). Does gromacs provide a way to cutoff coulomb potential at short range, i.e. below a certain radius, the coulombic potential stays constant instead of decreasing to negative infinity? I can't seem to find any options that would do this. Thanks, Adam -- 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] covariance map for all residues
Hi Dear all I want to draw covariance map using gromacs, so I have two questions: 1- I used the following command,but x and y axis show based on atom: gmx covar -s md.tpr -f md.trr -o eigenval.xvg -v eigenvect.trr -xpma covara.xpm the number of atoms on the x and y axis is less than total atom numbers in the pdb files, why is there this conflict? 2- I want to determine covariance map based on residue number, please let me know which command can I used to solve this problem? thanks a lot best wishes -- *Marzieh DehghanPhD of BiochemistryInstitute of biochemistry and Biophysics (IBB)University of Tehran, Tehran- Iran.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RDF from NPT simulation?
On 11/2/17 7:28 AM, Sudip Das wrote: Dear Justin, Should I have to use any flag(s) with 'rdf' module to scale the coordinates for fixing the box size? I didn't find such flag in 'rdf' module. There are no special flags. GROMACS commands deal with box vectors intrinsically. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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 field / parameters for NADH, FMN
On 11/2/17 12:05 PM, Hermann, Johannes wrote: Dear Justin, dear all, thank you for your reply. I will test the web server when I have managed to generate the mol2 file for FMN. I had a look in the rtp file of charmm36 ff and I detected that there are three "NADHs": NAD1 , NAI, and NAD1. NAI is the pdb 3 letter code for the reduced form of NAD+ (https://www4.rcsb.org/ligand/NAI), i.e. NADH. However, both NAI and NADH in the rtp file have only 71 atoms, while they should have 73. Hence, if I am not mistaken, NAI and NADH are both NAD (not NADH or NAD+). Has anyone who is reading this a ff field which he can send me? This would save me a lot of time. Anyone using the CHARMM force field should go to the MacKerell website and download the CHARMM-formatted topology and parameter files - they contain full chemical names and text drawings of structures. Unfortunately, there is no easy way to port all of this stuff to GROMACS so it gets lost. But if you ever need clarification, go to the source. NAD1: oxidized NAD (so it is NAD+), net charge -1 NAI and NADH: reduced NAD (so it is NADH), net charge -2 I don't know the history of why there are both NAI and NADH residues. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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 field / parameters for NADH, FMN
Dear Justin, dear all, thank you for your reply. I will test the web server when I have managed to generate the mol2 file for FMN. I had a look in the rtp file of charmm36 ff and I detected that there are three "NADHs": NAD1 , NAI, and NAD1. NAI is the pdb 3 letter code for the reduced form of NAD+ (https://www4.rcsb.org/ligand/NAI), i.e. NADH. However, both NAI and NADH in the rtp file have only 71 atoms, while they should have 73. Hence, if I am not mistaken, NAI and NADH are both NAD (not NADH or NAD+). Has anyone who is reading this a ff field which he can send me? This would save me a lot of time. Thanks in advance! All the best Johannes On 30.10.2017 16:14, Justin Lemkul wrote: On 10/30/17 10:58 AM, Hermann, Johannes wrote: Dear all, I want to simulate a complex consisting of a protein, FMN, and NADH. I have two problems/questions: 1) In the "CHARMM36 all-atom force field (March 2017)" parameters for NADH are present. But apparently I am using a wrong atom naming convention (I copied / pasted NADH from a pdb entry): Fatal error: Atom PN in residue NADH 0 was not found in rtp entry NADH with 71 atoms while sorting atoms. How can I generate a appropriate input file for gromacs gmx2pdb? Make the PDB file atom names match those of the .rtp entry. It's a bit awkward but everyone seems to have a different convention for naming cofactor atoms. 2) I did not find FMN in the charmm36 force field. Can some recommend me a program to generate a parameter file? And how to proceed with it? If it's not in CHARMM, use CGenFF. There's a web server that will parametrize it (cgenff.paramchem.org) and tell you how good the topology is so you can decide if you need to do any manual parametrization. Download the .str -> .itp conversion script from the MacKerell lab webpage and you're ready for GROMACS. -Justin -- __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- 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] problem compiling gmx-2016.4 with CUDA on debian stable/stretch
hi, I just tried to install gmx (2015.4) on my desktop with vanilla debian (stable/stretch with the debian nvidia/cuda driver packages installed) as recommended in INSTALL ... prompt> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=/home/user/local/gromacs-2016-4-bin finishes without any complaints, but when doing: prompt> make -j 12 i get:[...][ 3%] Building NVCC (Device) object src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/libgromacs_generated_gpu_utils.cu.o In file included from /usr/include/cuda_runtime.h:78:0, from :0: /usr/include/host_config.h:119:2: Fehler: #error -- unsupported GNU version! gcc versions later than 5 are not supported! #error -- unsupported GNU version! gcc versions later than 5 are not supported! ^ [...] debian stable has gcc-6 as default gcc, und there appears to be no gcc-4 or 5 in the standard debian repositories(apt-get install gcc-4.9 does not work) ... I understand installing two different gcc versions on one system can be difficult ...has anybody managed to successfully install gmx+CUDA/GPU support on debian stretch?? cheersmic -- 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] Problem using gmx wham
Hi Justin, Thanks for the response. The .dat files were created with the vi text editor, they contain lists of the .tpr and .xvg to be read, e.g. umbrella0.tpr umbrella1.tpr umbrella2.tpr .. umbrella52.tpr I've tried to use dos2unix, i.e. ~> dos2unix tpr-files.dat and ~> dos2unix pullf-files.dat but I still get the same error message i.e. --- Program gmx wham, VERSION 5.1.2 Source code file: /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 1800 Fatal error: Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- That being said, it seems you're correct in thinking something's weird with the input files. After I created new .dat files, I got this message: --- Program gmx wham, VERSION 5.1.2 Source code file: /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 3610 Fatal error: Found 53 file names in tpr-files.dat, but 54 in pullf-files.dat For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- gmx wham is registering 54 files, when only 53 were written. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Thursday, November 02, 2017 11:10 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem using gmx wham On 11/1/17 4:26 PM, Jefferies D.F. wrote: > Hi, > > I am attempting to use gmx wham to compute a potential of mean force. I have > used the command line: > > gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ > > where tpr-files.dat and pullf-files.dat contain a list of the .tpr and > pullf.xvg files from each umbrella sampling window, respectively. > > It seems that gmx wham is having trouble reading the .tpr and .xvg files, as > I get this error message: > > --- > > Program gmx wham, VERSION 5.1.4 > > Source code file: > /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp, > line: 1800 > > > Fatal error: > > Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo. > The extra space after "tpr" in the printed error suggests something is weird with the input .dat file. Did you create it with a proper plain text editor? What about running dos2unix on it to make sure you've got the right kind of line endings? -Justin > For more information and tips for troubleshooting, please check the GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > --- > > > I have computed potential of mean force profiles before (using this Mac), but > I haven't encountered this problem. Could someone help me with this problem? > > -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Umbrella Sampling Replica Exchange
Dear all, I was surprised that my Google search for Replica Exchange for Umbrella sampling using Gromacs did not yield a positive result. Is it really not possible to perform HRE for US within the framework of Gromacs? Thanks in advance for any answer, hint, or tutorial! All the best Johannes -- __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- 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 from NPT simulation?
Dear Justin, Should I have to use any flag(s) with 'rdf' module to scale the coordinates for fixing the box size? I didn't find such flag in 'rdf' module. Please help. Regards, Sudip On Thu, Nov 2, 2017 at 4:41 PM, Justin Lemkul wrote: > > > On 11/2/17 6:39 AM, Sudip Das wrote: > >> Dear All, >> >> Is it possible to calculate RDF from GROMACS module 'rdf' from a NPT >> simulation trajectory (where box size changes from frame to frame)? >> > Yes. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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] force field for selinomethionine?
As far as I see others just replace selenium with sulphur, convert of selenomethionine to methionine like:https://bmccancer.biomedcentral.com/articles/10.1186/1471-2407-14-775 On Wednesday, November 1, 2017, 8:24:10 AM GMT+2, Seera Suryanarayana wrote: Dear gromacs users, I have to do simulations for a peptide which has the selinomethionine. But regular force fields from gromacs has no information for this residue. kindly give me information if is there any force field for selinometheoinine. Thanks in advance Surya Graduate student India. -- 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 from NPT simulation?
On 11/2/17 6:39 AM, Sudip Das wrote: Dear All, Is it possible to calculate RDF from GROMACS module 'rdf' from a NPT simulation trajectory (where box size changes from frame to frame)? Yes. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Problem using gmx wham
On 11/1/17 4:26 PM, Jefferies D.F. wrote: Hi, I am attempting to use gmx wham to compute a potential of mean force. I have used the command line: gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ where tpr-files.dat and pullf-files.dat contain a list of the .tpr and pullf.xvg files from each umbrella sampling window, respectively. It seems that gmx wham is having trouble reading the .tpr and .xvg files, as I get this error message: --- Program gmx wham, VERSION 5.1.4 Source code file: /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp, line: 1800 Fatal error: Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo. The extra space after "tpr" in the printed error suggests something is weird with the input .dat file. Did you create it with a proper plain text editor? What about running dos2unix on it to make sure you've got the right kind of line endings? -Justin For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I have computed potential of mean force profiles before (using this Mac), but I haven't encountered this problem. Could someone help me with this problem? -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Amino Acids
On 11/2/17 7:07 AM, rose rahmani wrote: Yes,sir ;) Termini?! nothing is mentioned about it! Check again. "The AAs considered in the simulations are endowed with the acetyl group at the N-terminus and N-methylamide group at the C-terminus. These caps eliminate the terminal charges and mimic the presence of a peptide chain in which the AA exists in the unionized form (see, e.g., Refs. 15 and 46)." -Justin Sent from my iPhone On Nov 1, 2017, at 11:39, Mark Abraham wrote: Hi, Please try to keep to one email per question :-) Did you read the paper to learn what termini they used? Mark On Wed, 1 Nov 2017 07:34 rose rahmani wrote: Hi If standalone amino acids are zwitterionic and inappropriate for AMBER and GROMACS ,what do you think about this article?! Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations *Article* in The Journal of Chemical Physics 140(9):095101 · March 2014 DOI: 10.1063/1.4866763 · Source:PubMed < https://www.researchgate.net/publication/deref/http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpubmed%2F24606380 -- 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. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Amino Acids
Yes,sir ;) Termini?! nothing is mentioned about it! Sent from my iPhone > On Nov 1, 2017, at 11:39, Mark Abraham wrote: > > Hi, > > Please try to keep to one email per question :-) Did you read the paper to > learn what termini they used? > > Mark > >> On Wed, 1 Nov 2017 07:34 rose rahmani wrote: >> >> Hi >> >> If standalone amino acids are zwitterionic and inappropriate for AMBER and >> GROMACS ,what do you think about this article?! >> >> Interactions of aqueous amino acids and proteins with the (110) surface of >> ZnS in molecular dynamics simulations >> *Article* in The Journal of Chemical Physics 140(9):095101 · March 2014 >> DOI: 10.1063/1.4866763 · Source:PubMed >> < >> https://www.researchgate.net/publication/deref/http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpubmed%2F24606380 >> -- >> 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] how to do neutralization?
That can't be right, AMBER03 does not contain amino acid residues with partial charges. Each residue's charge is parametrized for a final integer net charge. Are you using any custom/modified residue blocks? If not, when you pass the PDB of a protein to pdb2gmx, and that protein containing aa. residues that are defined in the force field rtp file, pdb2gmx will produce a topology with integer net charge. It is generally a good idea to tell pdb2gmx to ignore the hydrogen atoms present in the PDB file and set the protonation states on the fly (using the -ignh and -inter flags). Now, if you're tampering with the rtp and itp files and/or parametrizing it yourself, that's a completely different story. AMBER03 and GROMACS are not to blame, it must be whatever the user is doing. From experience, I can tell you that a properly performed parametrization will yield no such issues. But it's difficult to evaluate the problem you're trying to describe without further detail. J On Thu, Nov 2, 2017 at 11:31 AM, rose rahmani wrote: > HI, > I have the same problem,i use AMBER03 force field,the structure has Zn and > S atoms and amino acids with net charge less than 1, idont know what should > i do,i optimized the structure in Gaussian and put H atom for make it more > stable but its not included in itp file. > > On Thu, Nov 2, 2017 at 1:23 PM, João Henriques < > joao.m.a.henriq...@gmail.com > > wrote: > > > Hi, > > > > What system is that and what force field are you using? Building blocks > > usually have integer net charges, this is rather unusual. > > > > Cheers, > > J > > > > On Thu, Nov 2, 2017 at 10:02 AM, Seera Suryanarayana < > paluso...@gmail.com> > > wrote: > > > > > Dear gromacs users > > > > > > I got the system non-zero total charge: -0.226000. When I add one NA > ion > > to > > > the system I got non-zero total charge: +0.77. What is the way to > > > neutralize the system? > > > > > > Thanks in advance > > > Surya > > > Graduate student > > > India. > > > -- > > > 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.
[gmx-users] RDF from NPT simulation?
Dear All, Is it possible to calculate RDF from GROMACS module 'rdf' from a NPT simulation trajectory (where box size changes from frame to frame)? Thanks in advance. Regards, Sudip -- 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] how to do neutralization?
HI, I have the same problem,i use AMBER03 force field,the structure has Zn and S atoms and amino acids with net charge less than 1, idont know what should i do,i optimized the structure in Gaussian and put H atom for make it more stable but its not included in itp file. On Thu, Nov 2, 2017 at 1:23 PM, João Henriques wrote: > Hi, > > What system is that and what force field are you using? Building blocks > usually have integer net charges, this is rather unusual. > > Cheers, > J > > On Thu, Nov 2, 2017 at 10:02 AM, Seera Suryanarayana > wrote: > > > Dear gromacs users > > > > I got the system non-zero total charge: -0.226000. When I add one NA ion > to > > the system I got non-zero total charge: +0.77. What is the way to > > neutralize the system? > > > > Thanks in advance > > Surya > > Graduate student > > India. > > -- > > 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] how to do neutralization?
Hi, What system is that and what force field are you using? Building blocks usually have integer net charges, this is rather unusual. Cheers, J On Thu, Nov 2, 2017 at 10:02 AM, Seera Suryanarayana wrote: > Dear gromacs users > > I got the system non-zero total charge: -0.226000. When I add one NA ion to > the system I got non-zero total charge: +0.77. What is the way to > neutralize the system? > > Thanks in advance > Surya > Graduate student > India. > -- > 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] how to do neutralization?
Dear gromacs users I got the system non-zero total charge: -0.226000. When I add one NA ion to the system I got non-zero total charge: +0.77. What is the way to neutralize the system? Thanks in advance Surya Graduate student India. -- 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.
