Re: [gmx-users] pdb2gmx and periodic molecule
Hi Alex, I think the best way is to extend the chain, such that you get an overlap between both ends. So for a stretch of DNA ACGT You would generate TACGTA Then you strip off the terminal atoms and rewire the links over the boundary. It requires renumbering the topology and at first looks a bit cumbersome, but this ensures all the links are correct and the modifications of the termini have no effect, and it's not very hard to script. And, of course, scripting it is a one time effort to avoid doing it manually later. Cheers, Tsjerk On Apr 26, 2015 5:55 AM, "Alex" wrote: > JL> The force field parameters for a phosphodiester are the same in a > linear, finite > JL> DNA as they will be in your infinite chain. > > I didn't mean that anything would need to be changed in the description of > residues. The FF handles a > finite chain perfectly. > > JL> The problem is in telling pdb2gmx > JL> "don't link i,i+1 here, instead link i,i+(some number of intervening > nucleotides)." > > This is exactly what I meant, the linking. Is there a way to achieve this > without messing with the code? I just haven't looked at the code, so > if you think I'm being a cheeky little bastard, I'll accept that. :) > > 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. > -- 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 name HIS in the input pdb for the pdb2gmx
Dear All， If we change HIS188 in Chain B to HISE188 in Chain B, before change the PDB looks like "HIS B 188", but after change the PDB will look like "HISEB 188", which makes thereis no space between "HISE" and "Bchain". I do not know whether pdb2gmx can recognize HISEB 188, or we process it in some other way. I am looking forward to getting a reply from you. Brett At 2015-04-26 11:08:19, "Justin Lemkul" wrote: > > >On 4/25/15 11:05 PM, Brett wrote: >> Dear All, >> >> For gromacs, for HIS residues there are HISD,HISE and HISH. In the original >> PDB file, are HIS residues are written as HIS. If based on necessity, I >> change exactly some HIS to HISD, some HIS to HISE and some HIS to HISH,the >> coordinate lines contaning HISD,HISE and HISH will not aling with all the >> other coordinate lines. Does pdb2gmx recognize these non-aligned coordinate >> lines? Or what other strategy you recommend me to take so that pdb2gmx can >> recognize HISD,HISE and HISH? >> > >Do the replacement properly and don't screw up column alignment. It needs to >be >correct for proper interpretation of the coordinates. > >-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. -- 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] pdb2gmx and periodic molecule
JL> The force field parameters for a phosphodiester are the same in a linear, finite JL> DNA as they will be in your infinite chain. I didn't mean that anything would need to be changed in the description of residues. The FF handles a finite chain perfectly. JL> The problem is in telling pdb2gmx JL> "don't link i,i+1 here, instead link i,i+(some number of intervening nucleotides)." This is exactly what I meant, the linking. Is there a way to achieve this without messing with the code? I just haven't looked at the code, so if you think I'm being a cheeky little bastard, I'll accept that. :) 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] pdb2gmx and periodic molecule
On 4/25/15 11:34 PM, Alex wrote: Justin, I am not entirely sure I understand your sequence of steps. Why do you want to first run it normally, but then also without adding the hydrogens? The hydrogens (a total of two) are only added at the termini by default, and in the final product there's no need for them anyway. I was speaking in generalizations; most starting structures need H added. If that's not relevant, then just skip it. Here's what I'm able to understand: run as usual, delete all bonded data relevant to termini, add bonded descriptions for the residues at the boundary, modify pdb to remove termini (actually, I can generate the periodic ones automatically). Am I missing something that should make my life easier? In theory, if you assign a phosphate as one of your termini (rather than the normal C5'-OH and C3'-OH) then you have to modify very little. Also, is there a way to automate this by modifying the forcefield? See, right now (on the periodic structure without termini) pdb2gmx sees the first residue and looks it up as one with a terminus, which is really the gist of the error it throws, so I doubt it even gets to the point of looking at the boundary. Is it that the utility behavior cannot be changed at the ff level, and thus our only option is manual modification of the topology? It's got nothing to do with the force field and everything to do with software and convention. It's the same case with cyclic peptides or circular DNA. It can be made to work, but that's not really how the software was designed because it's not a common procedure. DNA is assumed to be a linear polymer of finite length. If you don't do that, it's up to you to hack it together. The force field parameters for a phosphodiester are the same in a linear, finite DNA as they will be in your infinite chain. The problem is in telling pdb2gmx "don't link i,i+1 here, instead link i,i+(some number of intervening nucleotides)." -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.
Re: [gmx-users] pdb2gmx and periodic molecule
Justin, I am not entirely sure I understand your sequence of steps. Why do you want to first run it normally, but then also without adding the hydrogens? The hydrogens (a total of two) are only added at the termini by default, and in the final product there's no need for them anyway. Here's what I'm able to understand: run as usual, delete all bonded data relevant to termini, add bonded descriptions for the residues at the boundary, modify pdb to remove termini (actually, I can generate the periodic ones automatically). Am I missing something that should make my life easier? Also, is there a way to automate this by modifying the forcefield? See, right now (on the periodic structure without termini) pdb2gmx sees the first residue and looks it up as one with a terminus, which is really the gist of the error it throws, so I doubt it even gets to the point of looking at the boundary. Is it that the utility behavior cannot be changed at the ff level, and thus our only option is manual modification of the topology? Thank you, Alex JL> pdb2gmx isn't designed to intuitively handle such cases. The best way to go JL> about it is: JL> 1. Run pdb2gmx normally to add H that you might need and to apply patching such JL> that you have a phosphate on one end and an alcohol on the other (presumably you JL> already have this last part done and have suitable .tdb entries). JL> 2. Delete unnecessary atoms from the termini. JL> 3. Run pdb2gmx again with -ter (choose None) and -missing so that it doesn't JL> complain at you about dangling termini. JL> 4. Manually edit the topology to introduce the needed bond, angles, and dihedrals. JL> -Justin -- 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] Optimal GPU setup for workstation with Gromacs 5
Hi Carsten, Thank you so much for the invaluable advice, I'll go for the GTX 980 then. JJ -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Kutzner, Carsten Sent: Saturday, April 25, 2015 5:03 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Optimal GPU setup for workstation with Gromacs 5 > On 25 Apr 2015, at 03:39, Jingjie Yeo (IHPC) wrote: > > Hi Carsten, > > Thank you so much for the information! Seems like the GTX is the way to go. > One last question, regarding the Maxwell architecture, would there be any > kind of backward compatibility issue, say if I need to use both Gromacs 4.6 > and 5.0, since it is the newest architecture? No problem there. Both 4.6 and 5.0 work fine with GTX 980. Carsten > > JJ > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf > Of Kutzner, Carsten > Sent: Friday, April 24, 2015 5:51 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Optimal GPU setup for workstation with > Gromacs 5 > > Hi JJ, > >> On 24 Apr 2015, at 10:53, Jingjie Yeo (IHPC) >> wrote: >> >> Hi Carsten, >> >> Thank you so much for the information! I checked with my vendor on his >> opinions on the GTX and his reply was that GTX cards will not minimize >> calculation errors the way Tesla and Quadro cards will. Do you think this is >> an issue? > The GeForce cards do not offer ECC memory, so they cannot pick up > memory errors occurring on the GPU, which are however very unlikely. > Run an extensive memory check (e.g. memtestCL) before first usage of > the cards. We have tested nearly > 300 GeForce cards, and only 7 of them had problems with memory, so we > replaced them. > > Carsten > > >> >> JJ >> >> -Original Message- >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf >> Of Kutzner, Carsten >> Sent: Friday, 24 April, 2015 16:40 >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] Optimal GPU setup for workstation with >> Gromacs 5 >> >> Hi JJ, >> >>> On 24 Apr 2015, at 03:02, Jingjie Yeo (IHPC) >>> wrote: >>> >>> Hi Carsten, >>> >>> In this case of 2 x GTX980, as far as I can tell, the clock speed >>> and GPU ram is significantly lower. For simulations of more >> The GTX 980s have a clock rate of about 1200 MHz, whereas the clock rate of >> the Tesla K40 is 732 MHz. The latter has more CUDA cores, however. >> A rough estimate on how well the GROMACS short-ranged kernels perform on a >> card is the product of clock rate and CUDA cores. In this metric, the GTX >> 980 is slightly better than the K40. In addition, the GTX 980 also has the >> newer Maxwell generation chip, yielding somewhat higher performance due to >> better instruction scheduling. >> >> The amount of GPU memory is almost never an issue with GROMACS unless you >> want to run enormously large MD systems. The largest system that we >> benchmarked had 12 million atoms and this was using 1.2 GB of GPU memory, so >> you could even run a couple of these on a 980. >> >> In our tests with a 2 million atom system on a node with 2x E5-2680v2 >> processors, using two 980s resulted in a 14% increased GROMACS performance >> when compared to using two K40s. >> >> Note that from the money you save by buying GTX instead of Tesla >> cards you can get another node to run another simulation on :) >> >> Carsten >> >> >>> than a million atoms, would it be advisable to go for more cores or more >>> clock speed, or having both is the best case scenario? >>> >>> JJ >>> >>> -Original Message- >>> Date: Thu, 23 Apr 2015 08:03:46 + >>> From: "Kutzner, Carsten" >>> To: "gmx-us...@gromacs.org" >>> Subject: Re: [gmx-users] Optimal GPU setup for workstation with >>> Gromacs 5 >>> Message-ID: >>> Content-Type: text/plain; charset="us-ascii" >>> >>> Hi, >>> On 23 Apr 2015, at 08:03, Jingjie Yeo (IHPC) wrote: Dear all, My workstation specs are 2 x Intel Xeon E5-2695v2 2.40 GHz, 12 Cores. I would like to combine this with an optimal GPU setup for Gromacs 5 running simulations with millions of atoms. May I know what are the recommended setups? My vendor proposed doing a dual K40 Tesla GPU setup, would that be optimal? >>> I would propose to put two GTX 980 into that machine instead. >>> This will give you the same GROMACS performance at a fraction of the price. >>> >>> Carsten >>> Best Regards, JJ -- 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.
Re: [gmx-users] how to name HIS in the input pdb for the pdb2gmx
On 4/25/15 11:05 PM, Brett wrote: Dear All, For gromacs, for HIS residues there are HISD,HISE and HISH. In the original PDB file, are HIS residues are written as HIS. If based on necessity, I change exactly some HIS to HISD, some HIS to HISE and some HIS to HISH,the coordinate lines contaning HISD,HISE and HISH will not aling with all the other coordinate lines. Does pdb2gmx recognize these non-aligned coordinate lines? Or what other strategy you recommend me to take so that pdb2gmx can recognize HISD,HISE and HISH? Do the replacement properly and don't screw up column alignment. It needs to be correct for proper interpretation of the coordinates. -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.
Re: [gmx-users] Constraints and Energy Minimization
On 4/25/15 11:01 PM, Eric Smoll wrote: Hello Dr Lemkul, Thank you for the rapid response. It is much appreciated. On the subject of specifying constraints, how does the mdp keyword-value pair: "constraints=h-bonds" work? How are the bonds with hydrogen detected? By atom name. If the first character is 'H' it is converted to a constraint. Here are a few lines from ffnonbonded.itp in the oplsaa.ff. The atoms shown are for custom hydrogen additions to the opls forcefield. Note that the "bond_type" field begins with the element letter (in this case, "C" and "H") and has a suffix. [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_972CA_C 6 12.01100-0.130 A3.55000e-01 2.92880e-01 ;SIG opls_973HA_C 1 1.00800 0.210 A2.42000e-01 1.25520e-01 ;SIG This is only relevant for specifying, e.g. a bond in [bondtypes] between CA_C and HA_C. If I understand your original question right, there are no parameters for these bonds, so this really isn't relevant. Similarly, here are a few lines from the topology I have built. Note that I prefer to have the "atom" field list the chemical element (again "C" and "H") followed by a numerical suffix. In general my ffnonbonded "bond_type" field and the topology "atom" field do not match and are never just labeled with the element name. [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1096 opls_972 42CCC C5332 -0.13 12.011 ; qtot -13.07 1097 opls_973 42CCC H6332 0.21 1.008 ; qtot -12.86 Will "constraints=h-bonds" correctly identify C-H bonds in my system without manually adding to the topology? Yes. If a bond is listed between the atoms, it will be converted. -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.
[gmx-users] how to name HIS in the input pdb for the pdb2gmx
Dear All, For gromacs, for HIS residues there are HISD,HISE and HISH. In the original PDB file, are HIS residues are written as HIS. If based on necessity, I change exactly some HIS to HISD, some HIS to HISE and some HIS to HISH,the coordinate lines contaning HISD,HISE and HISH will not aling with all the other coordinate lines. Does pdb2gmx recognize these non-aligned coordinate lines? Or what other strategy you recommend me to take so that pdb2gmx can recognize HISD,HISE and HISH? I am looking forward to getting your reply. Brett -- 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] Constraints and Energy Minimization
Hello Dr Lemkul, Thank you for the rapid response. It is much appreciated. On the subject of specifying constraints, how does the mdp keyword-value pair: "constraints=h-bonds" work? How are the bonds with hydrogen detected? Here are a few lines from ffnonbonded.itp in the oplsaa.ff. The atoms shown are for custom hydrogen additions to the opls forcefield. Note that the "bond_type" field begins with the element letter (in this case, "C" and "H") and has a suffix. [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_972CA_C 6 12.01100-0.130 A3.55000e-01 2.92880e-01 ;SIG opls_973HA_C 1 1.00800 0.210 A2.42000e-01 1.25520e-01 ;SIG Similarly, here are a few lines from the topology I have built. Note that I prefer to have the "atom" field list the chemical element (again "C" and "H") followed by a numerical suffix. In general my ffnonbonded "bond_type" field and the topology "atom" field do not match and are never just labeled with the element name. [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1096 opls_972 42CCC C5332 -0.13 12.011 ; qtot -13.07 1097 opls_973 42CCC H6332 0.21 1.008 ; qtot -12.86 Will "constraints=h-bonds" correctly identify C-H bonds in my system without manually adding to the topology? Best, Eric On Sat, Apr 25, 2015 at 8:27 PM, Justin Lemkul wrote: > > > On 4/25/15 10:25 PM, Eric Smoll wrote: > >> Hello Gromacs Users, >> >> I am studying a forcefield where certain bond force constants were not >> specified because the associated bond lengths were "constrained." What do >> I >> need to do to run a simulation that is consistent with the way this >> forcefield was designed? Will LINCS constraints satisfy this requirement >> faithfully? >> >> > Specify [constraints] in the topology with the correct length. LINCS will > satisfy it; that's what it was designed to do. > > In a molecular dynamics workflow, when are constraints best introduced? >> For >> example, should constraints be used during energy minimization? >> >> > Sounds like your force field requires it, so there's really no question. > > In general, I say if you're going to run the MD with constraints, you need > to minimize with constraints. All too often I have seen bad geometries > come from unconstrained EM, which upon starting MD with constraints, cause > failure. An initial EM without constraints may be needed if the initial > geometry is really bad, but a subsequent constrained minimization is a good > idea in that case. > > -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. > -- 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] Constraints and Energy Minimization
On 4/25/15 10:25 PM, Eric Smoll wrote: Hello Gromacs Users, I am studying a forcefield where certain bond force constants were not specified because the associated bond lengths were "constrained." What do I need to do to run a simulation that is consistent with the way this forcefield was designed? Will LINCS constraints satisfy this requirement faithfully? Specify [constraints] in the topology with the correct length. LINCS will satisfy it; that's what it was designed to do. In a molecular dynamics workflow, when are constraints best introduced? For example, should constraints be used during energy minimization? Sounds like your force field requires it, so there's really no question. In general, I say if you're going to run the MD with constraints, you need to minimize with constraints. All too often I have seen bad geometries come from unconstrained EM, which upon starting MD with constraints, cause failure. An initial EM without constraints may be needed if the initial geometry is really bad, but a subsequent constrained minimization is a good idea in that case. -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.
[gmx-users] Constraints and Energy Minimization
Hello Gromacs Users, I am studying a forcefield where certain bond force constants were not specified because the associated bond lengths were "constrained." What do I need to do to run a simulation that is consistent with the way this forcefield was designed? Will LINCS constraints satisfy this requirement faithfully? In a molecular dynamics workflow, when are constraints best introduced? For example, should constraints be used during energy minimization? Best, Eric -- 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] pdb2gmx and protonated states of the residues
Aside from interacting with solvent-dissolved protons (if you add them), the protonation states are permanent in GMX. All forcefields used in these simulators are non-reactive (beyond vdw and electrostatics). Unless you run your simulation in stages, where you manually change protonation states, nothing chanes. Alex B> Dear All, B> B> By H++ and reduce we can have the input PDB for pdb2gmx have the B> initial corrected protonated states for some residues, for example, B> HIS, ARG, GLU and terminal residues. However biologically speaking with the change of the protein B> conformation, the protonated states of the above residues can be changed. B> B> Will you please introduce to me how GROMACS deal with the possible B> protonation state change during the MD process? B> B> Brett -- 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] pdb2gmx and protonated states of the residues
Dear All, By H++ and reduce we can have the input PDB for pdb2gmx have the initial corrected protonated states for some residues, for example, HIS, ARG, GLU and terminal residues. However biologically speaking with the change of the protein conformation, the protonated states of the above residues can be changed. Will you please introduce to me how GROMACS deal with the possible protonation state change during the MD process? Brett -- 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] Using thermostats to create temperature gradient in system
Hello Users I have equilibrated a protein solvent system using NVT ensemble and V - rescale thermostat. Target temperature was 300 K. Now I want to establish a temperature gradient in my system as follows : 1. Use Two Berendsen thermostats separately for Protein and Non Protein grps. Protein grp , T = 400 K Non protein grp, T = 300 K. Run in NVT for 100 ps. 2. Then remove thermostat from Protein grp. But keep thermostat for Non Protein grp. Run in NVT for 500 ps. I hope that the protein will come down or relax to 300 K. Is the above scheme feasible ? I have not yet tried. I use COM motion removal for the whole system. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- 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] mail about g_energy parameter
On 4/25/15 11:53 AM, vidhya sankar wrote: Dear justin thank you for your reply i used the following parameter in my mdp file cutoff-scheme= Group rlist= 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.4 rvdw = 1.4 When i do g_energy analysis to find out LJ-SR nad Lj-SR between CYCLIPEPTIDE1 and CNT it shows the negative value -311.9and -2.45122 J-SR:CYCLIPEPTIDE1-CNT -311.91.518.6465 -5.28722 (kJ/mol) LJ-LR:CYCLIPEPTIDE1-CNT-2.45122 0.019 0.265088 0.0560281 (kJ/mol) LJ-SR:CYCLIPEPTIDE2-CNT-312.105 319.4763 -5.26101 (kJ/mol)LJ-LR:CYCLIPEPTIDE2-CNT-2.69093 0.0077 0.0788448 -0.045267 (kJ/mol)LJ-SR:CYCLIPEPTIDE3-CNT-322.101 0.9818.11227.01285 (kJ/mol) LJ-LR:CYCLIPEPTIDE3-CNT-2.41642 0.023 0.236337 0.0742594 (kJ/mol) can i take LJ-LR parameter for analysing and discussion the problem ? . Because My g_ dist analysis shows the Distance between selected groups is is greater than 3.7 nm This value is less than 0.9 & 1.4 ( as described in Mdp file) I already answered this question: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096844.html These are atom-atom interaction energies within those groups; g_dist gives you COM distances between the groups, so you can't correlate the two. -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.
[gmx-users] mail about g_energy parameter
Dear justin thank you for your reply i used the following parameter in my mdp file cutoff-scheme= Group rlist= 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.4 rvdw = 1.4 When i do g_energy analysis to find out LJ-SR nad Lj-SR between CYCLIPEPTIDE1 and CNT it shows the negative value -311.9and -2.45122 J-SR:CYCLIPEPTIDE1-CNT -311.91.518.6465 -5.28722 (kJ/mol) LJ-LR:CYCLIPEPTIDE1-CNT-2.45122 0.019 0.265088 0.0560281 (kJ/mol) LJ-SR:CYCLIPEPTIDE2-CNT-312.105 319.4763 -5.26101 (kJ/mol)LJ-LR:CYCLIPEPTIDE2-CNT-2.69093 0.0077 0.0788448 -0.045267 (kJ/mol)LJ-SR:CYCLIPEPTIDE3-CNT-322.101 0.9818.11227.01285 (kJ/mol) LJ-LR:CYCLIPEPTIDE3-CNT-2.41642 0.023 0.236337 0.0742594 (kJ/mol) can i take LJ-LR parameter for analysing and discussion the problem ? . Because My g_ dist analysis shows the Distance between selected groups is is greater than 3.7 nm This value is less than 0.9 & 1.4 ( as described in Mdp file) -- 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] pdb2gmx and periodic molecule
Yeah, I was trying to avoid that last part. You can tell by now how much I dislike uhm doing work. :) I'll try it, thanks. Alex JL> 4. Manually edit the topology to introduce the needed bond, angles, and dihedrals. JL> -Justin -- 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] pdb2gmx and the terminal residue
On 4/25/15 10:49 AM, Brett wrote: Dear All, For the pdb2gmx, if I will not assign charges to the N-terminal residue and C-terminal residue, I need to use pdb2gmx -ter, or I need to use pdb2gmx -[no]ter? The -ter option allows you to choose protonation state or no terminal processing if there are caps. In addition, whether there will be charges at the N-terminal residue and C-terminal residue has relation with the force field used, am I right? I don't understand this question. The individual partial charges on the atoms are indeed a function of the force field, but the choice of protonation state or capping is totally independent of the force field and is dictated by biological relevance. -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.
Re: [gmx-users] pdb2gmx and the Glu residue
On 4/25/15 10:40 AM, Brett wrote: Dear All, In the top file produced by H++ server for AMBER, if there is no charge for the Glu, the residue name will be modified to GLH. In our gromacs, we never treat Glu as without charge, thus we do not have GLH residue, am I right? No. You can treat glutamate however you like (and in this case, it sounds like it should be protonated). Different force fields call the residue different things. It's GLH in AMBER force fields, GLUH in GROMOS and OPLS-AA, and GLUP in CHARMM. Thus, all the force fields support the protonated form. -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.
[gmx-users] pdb2gmx and the Glu residue
Dear All, In the top file produced by H++ server for AMBER, if there is no charge for the Glu, the residue name will be modified to GLH. In our gromacs, we never treat Glu as without charge, thus we do not have GLH residue, am I right? Brett -- 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] pdb2gmx and the terminal residue
Dear All, For the pdb2gmx, if I will not assign charges to the N-terminal residue and C-terminal residue, I need to use pdb2gmx -ter, or I need to use pdb2gmx -[no]ter? In addition, whether there will be charges at the N-terminal residue and C-terminal residue has relation with the force field used, am I right? Brett -- 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] Pull code
Try constraint method. It works . Sent from my Huawei Mobile Alex wrote: That is not an option for me, all groups must exhibit full dynamics, so partial restraint seems like a decent option. It is my understanding that explicitly moving only one group is impossible in the new version. Is that the case? Thanks, Alex On Wed, Apr 22, 2015 at 5:58 PM, Ming Tang wrote: > Hi, Alex > > I tried this code plus freeze all of the atoms in the group needed to stay > in place, and it worked well. > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Alex > Sent: Thursday, 23 April 2015 9:47 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Pull code > > The CNT group is actually very strongly restrained, not the entire atomic > population, but the edges. So, from inspecting my code, everything looks > right? > > Thanks, > > Alex > > > > > >Not really. The constraint option keeps a rigid constraint between > > >the > > two groups. The "umbrella" keyword specifies a >harmonic potential, > > whose strength is tunable. Otherwise, the two methods are identical. > > > > >If one group needs to stay in place, it needs position restraints > > >applied > > to it. If the desired separation is not occurring, >either a larger > > spring force constant or a faster pull rate is needed. > > > > > >-Justin > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trjconv for cutting the trajectory in small subtrajectories
Thanks my friendsI checked new trajectory by gmxcheck and get following text: Reading frame 0 time 7000.000 # Atoms 8383 Precision 0.001 (nm) Reading frame 5000 time 17000.000 Item #frames Timestep (ps) Step 5501 2 Time 5501 2 Lambda 0 Coords 5501 2 Velocities 0 Forces 0 Box 5501 2 Reading frame is 5000 but desired frames are 5500 frame. I'm confused.best On Saturday, April 25, 2015 5:42 PM, James Lord wrote: Hi Mahboobeh,I recommend checking the created trajectories with gmx check. CheersJames On Sun, Apr 26, 2015 at 12:39 AM, Ming Tang wrote: Hi，-e is end frame， -b is the start one. Sent from my Huawei Mobile Mahboobeh Eslami wrote: hi GMx user I simulated protein-ligand comolex with gromacs. total simulation time is 20ns. when I use trjconv for cutting the trajectory in small subtrajectories from 1ps to 17000ps by following command: trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000 I see following text in terminal window; Reading frame 0 time 1.000 Precision of md-nopbc.xtc is 0.001 (nm) Using output precision of 0.001 (nm) -> frame 3500 time 17000.000 -> frame 3000 time 16000.000 I think the generated trajectory is incomplete because saved frame is incomplete. please guide me. Many thanks tobest -- 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] trjconv for cutting the trajectory in small subtrajectories
On 4/25/15 9:24 AM, Mahboobeh Eslami wrote: Thanks my friends I checked new trajectory by gmxcheck and get following text: Reading frame 0 time 7000.000 # Atoms 8383 Precision 0.001 (nm) Reading frame5000 time 17000.000 Item#frames Timestep (ps) Step 55012 Time 55012 Lambda 0 Coords55012 Velocities 0 Forces 0 Box 55012 Reading frame is 5000 but desired frames are 5500 frame. I'm confused. best Again, this is irrelevant; it's a buffered progress indicator that has a fixed interval for printing (1000 past a certain point). You have 5501 frames (5500 + the first, inclusive, so 5501). -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.
Re: [gmx-users] pdb2gmx and periodic molecule
On 4/25/15 12:00 AM, Alex wrote: Ahoy, What I have here is a 100% precisely set up periodic ssdna chain of six residues without termini. The goal is to get the 'polymerization' across the box. So, I boxed the chain and set up the periodicity pretty much perfectly. To test, translation in the direction of periodicity by the periodicity constant results in bonds perfectly recognized by things like VMD or pymol (in the concatenated structure). When running pdb2gmx on the boxed structure, the periodicity seems to be ignored and then expectedly I get a fatal error with a custom FF that works fine on finite chains. x2top sees pbc, but we're not using it here. So, no topology in sight. Any ideas? pdb2gmx isn't designed to intuitively handle such cases. The best way to go about it is: 1. Run pdb2gmx normally to add H that you might need and to apply patching such that you have a phosphate on one end and an alcohol on the other (presumably you already have this last part done and have suitable .tdb entries). 2. Delete unnecessary atoms from the termini. 3. Run pdb2gmx again with -ter (choose None) and -missing so that it doesn't complain at you about dangling termini. 4. Manually edit the topology to introduce the needed bond, angles, and dihedrals. -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.
Re: [gmx-users] trjconv for cutting the trajectory in small subtrajectories
Hi Mahboobeh, I recommend checking the created trajectories with gmx check. Cheers James On Sun, Apr 26, 2015 at 12:39 AM, Ming Tang wrote: > Hi，-e is end frame， -b is the start one. > > Sent from my Huawei Mobile > > Mahboobeh Eslami wrote: > > hi GMx user I simulated protein-ligand comolex with gromacs. total > simulation time is 20ns. when I use trjconv for cutting the trajectory > in small subtrajectories from 1ps to 17000ps by following command: > trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000 > I see following text in terminal window; > Reading frame 0 time 1.000 > Precision of md-nopbc.xtc is 0.001 (nm) > Using output precision of 0.001 (nm) > -> frame 3500 time 17000.000-> frame 3000 time 16000.000 > I think the generated trajectory is incomplete because saved frame is > incomplete. please guide me. > Many thanks tobest > -- > 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] pdb2gmx on HID HIE and HIP
On 4/25/15 5:35 AM, Brett wrote: Dear All, Will you please tell me which software or server can handle a PDB file so that the HIS residues in the original PDB file will be automatically changed into HID, HIE and HIP in the new PDB file, which can be processed by pdb2gmx, based on the H patten in the HIS residues in the original PDB file? Does "H pattern" mean the actual atoms or the hydrogen bonding network. If the former, that means you already have the H atoms built and you just need to change the residue names. If the latter, that's exactly what pdb2gmx does. -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.
Re: [gmx-users] About Analsysi tool
On 4/24/15 11:57 PM, vidhya sankar wrote: Dear Justin Thank you for your previous reply, I am doing Dynamics for CNT-wraapped by Cyclic peptide . The Cyclic peptide i am stacking Beyond Hydrogen bond distance. AT end of Simulation, the Assembly become Collapsed Is there is Any tool To list out interaction energy and analyze the interaction energy (may be decomposing during simulation) between Cyclic peptides and Between Cyclic peptides Vs CNT That is exactly what g_energy with energygrps is for. -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.
Re: [gmx-users] trjconv for cutting the trajectory in small subtrajectories
On 4/25/15 7:52 AM, Mahboobeh Eslami wrote: hi GMx user I simulated protein-ligand comolex with gromacs. total simulation time is 20ns. when I use trjconv for cutting the trajectory in small subtrajectories from 1ps to 17000ps by following command: trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000 I see following text in terminal window; Reading frame 0 time 1.000 Precision of md-nopbc.xtc is 0.001 (nm) Using output precision of 0.001 (nm) -> frame 3500 time 17000.000-> frame 3000 time 16000.000 The output frame number doesn't necessarily reflect what's actually written; it's just a simple progress indicator. Use gmxcheck to verify the contents of the new trajectory. -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.
Re: [gmx-users] trjconv for cutting the trajectory in small subtrajectories
hi dear mingYes. Sorry, I've used the following command:
trjconv -f md.xtc -s md.tpr -n index.ndx -b 1 -e 17000
but I do not get the desired result.best
On Saturday, April 25, 2015 5:09 PM, Ming Tang wrote:
#yiv1199526006 -- .yiv1199526006EmailQuote
{margin-left:1pt;padding-left:4pt;border-left:#80 2px solid;}#yiv1199526006
Hi，-e is end frame， -b is the start one.
Sent from my Huawei Mobile
Mahboobeh Eslami wrote:
hi GMx user I simulated protein-ligand comolex with gromacs. total simulation
time is 20ns. when I use trjconv for cutting the trajectory in small
subtrajectories from 1ps to 17000ps by following command:
trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000
I see following text in terminal window;
Reading frame 0 time 1.000
Precision of md-nopbc.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)
-> frame 3500 time 17000.000 -> frame 3000 time 16000.000
I think the generated trajectory is incomplete because saved frame is
incomplete. please guide me.
Many thanks tobest
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Re: [gmx-users] trjconv for cutting the trajectory in small subtrajectories
Hi，-e is end frame， -b is the start one. Sent from my Huawei Mobile Mahboobeh Eslami wrote: hi GMx user I simulated protein-ligand comolex with gromacs. total simulation time is 20ns. when I use trjconv for cutting the trajectory in small subtrajectories from 1ps to 17000ps by following command: trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000 I see following text in terminal window; Reading frame 0 time 1.000 Precision of md-nopbc.xtc is 0.001 (nm) Using output precision of 0.001 (nm) -> frame 3500 time 17000.000-> frame 3000 time 16000.000 I think the generated trajectory is incomplete because saved frame is incomplete. please guide me. Many thanks tobest -- 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] trjconv for cutting the trajectory in small subtrajectories
hi GMx user I simulated protein-ligand comolex with gromacs. total simulation time is 20ns. when I use trjconv for cutting the trajectory in small subtrajectories from 1ps to 17000ps by following command: trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000 I see following text in terminal window; Reading frame 0 time 1.000 Precision of md-nopbc.xtc is 0.001 (nm) Using output precision of 0.001 (nm) -> frame 3500 time 17000.000 -> frame 3000 time 16000.000 I think the generated trajectory is incomplete because saved frame is incomplete. please guide me. Many thanks tobest -- 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] pdb2gmx on HID HIE and HIP
Dear All, Will you please tell me which software or server can handle a PDB file so that the HIS residues in the original PDB file will be automatically changed into HID, HIE and HIP in the new PDB file, which can be processed by pdb2gmx, based on the H patten in the HIS residues in the original PDB file? I am looking forward to getting your reply. Best regards. Brett -- 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] Optimal GPU setup for workstation with Gromacs 5
> On 25 Apr 2015, at 03:39, Jingjie Yeo (IHPC) wrote: > > Hi Carsten, > > Thank you so much for the information! Seems like the GTX is the way to go. > One last question, regarding the Maxwell architecture, would there be any > kind of backward compatibility issue, say if I need to use both Gromacs 4.6 > and 5.0, since it is the newest architecture? No problem there. Both 4.6 and 5.0 work fine with GTX 980. Carsten > > JJ > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > Kutzner, Carsten > Sent: Friday, April 24, 2015 5:51 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Optimal GPU setup for workstation with Gromacs 5 > > Hi JJ, > >> On 24 Apr 2015, at 10:53, Jingjie Yeo (IHPC) >> wrote: >> >> Hi Carsten, >> >> Thank you so much for the information! I checked with my vendor on his >> opinions on the GTX and his reply was that GTX cards will not minimize >> calculation errors the way Tesla and Quadro cards will. Do you think this is >> an issue? > The GeForce cards do not offer ECC memory, so they cannot pick up memory > errors occurring on the GPU, which are however very unlikely. Run an > extensive memory check (e.g. memtestCL) before first usage of the cards. We > have tested nearly > 300 GeForce cards, and only 7 of them had problems with memory, so we > replaced them. > > Carsten > > >> >> JJ >> >> -Original Message- >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf >> Of Kutzner, Carsten >> Sent: Friday, 24 April, 2015 16:40 >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] Optimal GPU setup for workstation with >> Gromacs 5 >> >> Hi JJ, >> >>> On 24 Apr 2015, at 03:02, Jingjie Yeo (IHPC) >>> wrote: >>> >>> Hi Carsten, >>> >>> In this case of 2 x GTX980, as far as I can tell, the clock speed and >>> GPU ram is significantly lower. For simulations of more >> The GTX 980s have a clock rate of about 1200 MHz, whereas the clock rate of >> the Tesla K40 is 732 MHz. The latter has more CUDA cores, however. >> A rough estimate on how well the GROMACS short-ranged kernels perform on a >> card is the product of clock rate and CUDA cores. In this metric, the GTX >> 980 is slightly better than the K40. In addition, the GTX 980 also has the >> newer Maxwell generation chip, yielding somewhat higher performance due to >> better instruction scheduling. >> >> The amount of GPU memory is almost never an issue with GROMACS unless you >> want to run enormously large MD systems. The largest system that we >> benchmarked had 12 million atoms and this was using 1.2 GB of GPU memory, so >> you could even run a couple of these on a 980. >> >> In our tests with a 2 million atom system on a node with 2x E5-2680v2 >> processors, using two 980s resulted in a 14% increased GROMACS performance >> when compared to using two K40s. >> >> Note that from the money you save by buying GTX instead of Tesla cards >> you can get another node to run another simulation on :) >> >> Carsten >> >> >>> than a million atoms, would it be advisable to go for more cores or more >>> clock speed, or having both is the best case scenario? >>> >>> JJ >>> >>> -Original Message- >>> Date: Thu, 23 Apr 2015 08:03:46 + >>> From: "Kutzner, Carsten" >>> To: "gmx-us...@gromacs.org" >>> Subject: Re: [gmx-users] Optimal GPU setup for workstation with >>> Gromacs 5 >>> Message-ID: >>> Content-Type: text/plain; charset="us-ascii" >>> >>> Hi, >>> On 23 Apr 2015, at 08:03, Jingjie Yeo (IHPC) wrote: Dear all, My workstation specs are 2 x Intel Xeon E5-2695v2 2.40 GHz, 12 Cores. I would like to combine this with an optimal GPU setup for Gromacs 5 running simulations with millions of atoms. May I know what are the recommended setups? My vendor proposed doing a dual K40 Tesla GPU setup, would that be optimal? >>> I would propose to put two GTX 980 into that machine instead. >>> This will give you the same GROMACS performance at a fraction of the price. >>> >>> Carsten >>> Best Regards, JJ -- 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/mail
