[gmx-users] Re:Re: Re: Average box size
f the triclinic box vectors so that I can generate the > > triclinic box with the > > help of the corresponding angles (88.30, 107.40, 112.20) using the > > command "editconf". > > > > Now I understand that the box-x, box-y, and box-z represents the diagonal > > elements of triangular matrix and the average volume of my triclinic box > > is the product of these diagonal elements. However, as I understand the > > command "editconf" requires the length of the box vectors and the three > > angles > > to create a triclinic box. > > > > I would greatly appreciate if you could please let me know the command(s) > > that > > I would require to use to achieve my goal. > > > > > > > > > > Message: 4 > > Date: Tue, 4 Jan 2011 12:35:36 +0100 > > From: Tsjerk Wassenaar > > Subject: Re: [gmx-users] Re: Average box size > > To: Discussion list for GROMACS users > > Message-ID: > > > > Content-Type: text/plain; charset=ISO-8859-1 > > > > Hi Navjeet, > > > > These you had in the log file as you showed in your mail. Note that > > you use isotropic pressure coupling, so you just need to calculate a > > scaling factor, which you can give to editconf to change your system > > to match the average box size. > > > > Cheers, > > > > Tsjerk > > > > On Tue, Jan 4, 2011 at 12:03 PM, Navjeet Ahalawat > > wrote: > >> Hi Tsjerk, > >> > >> Thanks for reply, Please can you tell me how can I get the average box > >> length (a b c) of my triclinic box for my next step. > >> > >>> Message: 2 > >>> Date: Mon, 3 Jan 2011 18:17:15 +0100 > >>> From: Tsjerk Wassenaar > >>> Subject: Re: [gmx-users] Average box size > >>> To: Discussion list for GROMACS users > >>> Message-ID: > >>> > >>> Content-Type: text/plain; charset="iso-8859-1" > >>> > >>> Hi Navjeet, > >>> > >>> The box is defined as a triangular matrix, so the volume equals the > >>> product > >>> of the diagonal elements. > >>> > >>> Hope it helps, > >>> > >>> Tsjerk > >>> > >>> On Jan 3, 2011 5:57 PM, "Navjeet Ahalawat" wrote: > >>> > >>> Hi all > >>> > >>> I did NPT simulation for 30 ns using triclinic box (-angles 88.30, > >>> 107.40, 112.20) and Isotropic pressure coupling. Now i want to use > >>> average box size for production run (NVT). But I am confused because i > >>> am not able to get the meaning of the output values of the log file. > >>> > >>> > >>> Log file output. > >>> > >>> <== ### ==> > >>> < A V E R A G E S > > >>> <== ### ==> > >>> > >>> Energies (kJ/mol) > >>> Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 > >>> 9.31715e+02 2.35558e+03 1.63083e+02 5.15266e+03 1.79003e+03 > >>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential > >>> 1.63211e+04 2.86765e+04 -1.72320e+05 -4.98704e+04 -1.66800e+05 > >>> Kinetic En. Total Energy Temperature Pressure (bar) Cons. rmsd () > >>> 1.27874e+04 -1.54012e+05 1.49958e+02 1.07033e+00 0.0e+00 > >>> > >>> Box-X Box-Y Box-Z Volume Density (SI) > >>> 4.44479e+00 4.49781e+00 4.88259e+00 9.76118e+01 1.04364e+03 > >>> > >>> If Box-X Box-Y Box-Z represent average value of a b c then volume > >>> does not correspond to my triclinic box because its just > >>> multiplication of Box-X Box-Y Box-Z. So Please can anybody help me > >>> which volume should I consider for next NVT production run. > >>> > >>> Any help in this regard would be highly appreciated. > >>> > >>> > >>> Thanks & Regards, > >>> Navjeet Ahalawat > >> -- > >> gmx-users mailing list gmx-us...@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gm
Re: [gmx-users] Re:Re: Re: Average box size
-1.72320e+05 -4.98704e+04 -1.66800e+05 >> >>> Kinetic En. Total Energy Temperature Pressure (bar) Cons. rmsd () >> >>> 1.27874e+04 -1.54012e+05 1.49958e+02 1.07033e+00 0.0e+00 >> >>> >> >>> Box-X Box-Y Box-Z Volume Density (SI) >> >>> 4.44479e+00 4.49781e+00 4.88259e+00 9.76118e+01 1.04364e+03 >> >>> >> >>> If Box-X Box-Y Box-Z represent average value of a b c then volume >> >>> does not correspond to my triclinic box because its just >> >>> multiplication of Box-X Box-Y Box-Z. So Please can anybody help me >> >>> which volume should I consider for next NVT production run. >> >>> >> >>> Any help in this regard would be highly appreciated. >> >>> >> >>> >> >>> Thanks & Regards, >> >>> Navjeet Ahalawat >> >> -- >> >> gmx-users mailing list gmx-us...@gromacs.org >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> >> Please search the archive at >> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> >> Please don't post (un)subscribe requests to the list. Use the >> >> www interface or send it to gmx-users-requ...@gromacs.org. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > >> > -- >> > Tsjerk A. Wassenaar, Ph.D. >> > >> > post-doctoral researcher >> > Molecular Dynamics Group >> > * Groningen Institute for Biomolecular Research and Biotechnology >> > * Zernike Institute for Advanced Materials >> > University of Groningen >> > The Netherlands >> > >> > >> > -- >> > -- >> > gmx-users mailing list gmx-us...@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> > Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to gmx-users-requ...@gromacs.org. >> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> > -- next part -- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110106/5acc42a6/attachment.html > > -- > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 81, Issue 35 > * > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Question
Hello, running grompp gives me this error: Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/convparm.c, line: 325 Fatal error: unknown function type 20 in ../../../../src/kernel/convparm.c line 326 The two lines 325 and 326 of convparm.c are: break; case F_VSITE2: What can be the error? I never used function type 20. Thanks! Thomas -- GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit gratis Handy-Flat! http://portal.gmx.net/de/go/dsl -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Sampling windows
Hi Xavier Thanks very much for your time. That has mad things very clear Gavin Avier Periole wrote: > > On Jan 5, 2011, at 6:03 PM, Gavin Melaugh wrote: > >> Hi Xavier >> >> Many thanks. Two more quick questions (both refering to barrier region): >> Does the value of the force constant affect the height of the barrier >> providing that there is reasonable overlap? > No! The force constant used does not affect the PMF or the barrier. > Neither > does the number of windows used. The only thing that can affect your > PMF is a change in the sampling you put in ... >> Obviously there is a >> compromise between the size of the constant and the number of windows. > True! And the objective being to get equilibrated distribution with > reasonable > overlaps. >> If I increase the force constant and number of windows to obtain a high >> density of sampling, does this give a more accurate curve? > No! The only thing you need is to sample everything. Actually putting a > strong force constant might have the side effect to trap your system and > then you do not sample the "free" degrees of freedom! With weak force > constant you may have to wait very long to obtain an equilibrated > distribution. > > XAvier. >> >> Gavin >> >> XAvier Periole wrote: >>> >>> On Jan 5, 2011, at 5:01 PM, Gavin Melaugh wrote: >>> Hi Xavier Many thanks for the reply. When I compare the two curves Curve 1) lack of overlap in barrier region; force constant = 1000 Curve 2) with increased number of sampling windows with increased force constant (note I have only increased the force constant of the windows in the barrier region). Force constant =1000, Force constant in barrier region = 5000 The barrier increases due to better sampling in this region (expected), but the rest of the curve in 2) is shifted upward compared to curve 1). Why is this so when the only difference is the increased number of windows and force constant in one region? >>> the relative position of the regions on the left and right of your >>> "barrier" >>> region is completely depending on the barrier region! >>> >>> you may have overestimated the difference between bound/unbound states >>> because the energy barrier region was not sampled. >>> >>> Note also that cure one is simply wrong so comparing to it is >>> dangerous. >>> >>> You have to be careful that you might still not have a converged >>> sampling: >>> you might have overlap of your histograms on the reaction coordinate >>> but >>> other degrees of freedom are not fully sampled ... that might result >>> in a >>> funny and wrong profile. You might want to look at your simulations for >>> funny things ... >>> Gavin XAvier Periole wrote: > > On Jan 5, 2011, at 4:08 PM, Gavin Melaugh wrote: > >> Dear all >> >> I have generated a PMF curve for introducing a guest molecule into a >> host molecule using the umbrella sampling method. The curve seems >> fine, >> but there are no overlaps between histograms in the barrier >> region. To >> circumvent this I have added more windows in this region and to >> ensure >> sampling have increased the force constant only in this region. The >> windows in this problematic region are now not equally spaced. Does >> this >> matter for g_WHAM? > Nope it does not matter. >> Could someone please reply to me on this matter as it >> has been a sticking point for me for quite sometime? >> >> Many thanks >> Gavin >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search th
[gmx-users] Re: [ atomtypes ] are not case sensitive?
Dear GMX list, It's more the 2 years ago and now with my gmx.top file containing: [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 caca 0. 0. A 3.39967e-01 3.59824e-01 And using GMX 4.5 and I don't see this complain anymore: WARNING 1 [file system_GMX.top, line 43]: Overriding atomtype CA Should I assume that gromacs finally made its atomtypes case sensitive? Only version 4.5 and above? Many thanks, Alan On 21 August 2008 09:07, Alan wrote: > Well, I didn't developed Amber FF neither GAFF and although only Amber FF > is ported to GMX, one of the greatest appealing of Amber is its antechamber > and GAFF for generating topology for non usual compounds. > > Looking at the way GAFF was developed (remember G is for generalised) is > seemed a natural step to me to use the same name for atom types but using a > different cases. > > So have said that, I did a look at my converted topology file by > amb2gmx/acpypi and found that, although for vdw parameters they seem the > same, this doesn't hold for bonds for example. I have this in my GMX top > file: > > [ bonds ] > ... > 96 97 11.0800e-013.0711e+05 ;CZ2 - HZ2 (AT CA - HA) > Protein > ... > 3154 3194 11.0870e-012.8811e+05 ;C76 - H76 (AT ca - ha) > Ligand > > Anyway, after all this discussion, I realized (correct if I am wrong > please) that as long as the vdw parameters are the same, anything else is > NOT affected because even for the example of bonds above atom types change > nothing since parameters are explicit. > > Then, I decided to compare gaff.dat and parm99.dat (topology parameters > files for Amber package) for vdw. I did found 2 atom types with same name > (diff case though) and diff parameters: > > parm99.dat >HP 1.1000 0.0157 Veenstra et al JCC,8,(1992),963 >Na 1.8680 0.00277Na+ Aqvist JPC 1990,94,8021. > (adapted) > > gaff.dat >hp 0.6000 0.0157 same to hs (be careful !) >na 1.8240 0.1700 OPLS > > Observe by the comments (4th column) that although they have the same name > (but diff by case) they are completely unrelated, hence the diff values for > r0 and epsilon. > > So, in the end, at least for example gaff.dat x parm99.dat (note that Amber > has several others parm*.dat and glycam*.dat), I do have a conflicting case > issue that would affect my topology in GMX format if using amb2gmx/acpypi > tool for conversion. > > Pondering a bit more, I came to the conclusion that at least for acpypi > (which I am developing), I can make it aware of this conflicting atom type > naming issue and rename it when converting from Amber to GMX. > > About changing something in GMX? Frankly I don't know, but I hope that this > thread can be of some use for someone else who stumbles in this problem. > > Cheers and many thanks for attention dear Berk. > > Alan > > > From: Berk Hess >> Subject: RE: [gmx-users] RE: [ atomtypes ] are not case sensitive? >> Hi, >> >> I don't know if any thinking went into the (non) case specifity of atom >> types. >> Nearly all string comparisons in Gromacs are not case specific. >> For things like atom names this makes sense. >> >> We could change the atom type comparisons to case specific. >> I think that all force field files supplied with Gromacs have consistent >> cases. >> But some users might have made force fields where this would cause >> problems. >> >> I think it is bad practice to distinguish atom types just by case, >> this makes things quite error prone. >> But allowing this probably does not mean that many people would do this. >> >> Another option would be to add an option to grompp. >> >> Berk. >> >> >> Date: Tue, 19 Aug 2008 12:03:57 +0100 >> >> From: alanwil...@gmail.com >> To: gmx-users@gromacs.org >> Subject: [gmx-users] RE: [ atomtypes ] are not case sensitive? >> >> >> Dear Berk, >> Thanks for your attention. >> I don't know how familiar are you to amb2gmx and ffamber port to GMX. I am >> just learning since I am trying to test an application that is related to >> amb2gmx and ffamber (acpypi). >> >> So, for Amber MD (MD to contrast with FF), Generalised Amber Force Field >> (GAFF) uses all the atom types (AT) usually defined for Amber FF and several >> more AT but in lower case. I cannot assure 100% but I believe that for all >> common AT (being upper or lower), they share the same parameters including >> when found in bonds, angles etc. parameters. >> >> If so, then, it's not a problem if GMX is not sensitive about AT lower or >> upper case, because in the end they are the same. But, as I said before, I >> am not 100% sure about it. However, for Amber MD, case matters! >> >> Anyway, I am just worried about integrating Amber FF in GMX. If using >> ffamber port this problem doesn't appear because for Amber FF (f
[gmx-users] methanol simulation
Hi all, I have the following error in grompp before energy minimization: No such moleculetype SOL I have used grep to count the methanol molecules and added SOL 291 comment in .top file to tell the number of methanols. What is missing there? Note: I have used pdb2gmx -f xxx.pdb , that is, I haven't added anything like in water simulation -water tip3p. Should we add something to tell the gromacs that it is methanol simulation? best wishes mustafa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] methanol simulation
On 6/01/2011 10:35 PM, mustafa bilsel wrote: Hi all, I have the following error in grompp before energy minimization: No such moleculetype SOL I have used grep to count the methanol molecules and added SOL 291 comment in .top file to tell the number of methanols. What is missing there? Note: I have used pdb2gmx -f xxx.pdb , that is, I haven't added anything like in water simulation -water tip3p. Should we add something to tell the gromacs that it is methanol simulation? The [ molecules ] section of your .top lists the names you gave to the [ moleculetypes ] and the number of such molecules. Apparently you gave no moleculetype the name "SOL"... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Question
Thomas Koller wrote: Hello, running grompp gives me this error: Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/convparm.c, line: 325 Fatal error: unknown function type 20 in ../../../../src/kernel/convparm.c line 326 The two lines 325 and 326 of convparm.c are: break; case F_VSITE2: Not according to the 4.0.7 code; which version are you looking at? Line 325 is just the call to the fatal error. What can be the error? I never used function type 20. Something unknown has been found in your topology. Without seeing the topology, it's impossible to say what the problem is. -Justin Thanks! Thomas -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Question
On 6/01/2011 8:28 PM, Thomas Koller wrote: Hello, running grompp gives me this error: Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/convparm.c, line: 325 Fatal error: unknown function type 20 in ../../../../src/kernel/convparm.c line 326 The two lines 325 and 326 of convparm.c are: break; case F_VSITE2: Not in gromacs-4.0.7. You're looking at a different code version from that which is being executed. However that doesn't explain how the error is arising. My suspicion is that you might be running afoul of a dynamic linking mismatch between multiple GROMACS versions. Is this plausible? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Question
On 6/01/2011 8:28 PM, Thomas Koller wrote: Hello, running grompp gives me this error: Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/convparm.c, line: 325 Fatal error: unknown function type 20 in ../../../../src/kernel/convparm.c line 326 The two lines 325 and 326 of convparm.c are: break; case F_VSITE2: What can be the error? I never used function type 20. Actually, you have used it. Internal type 20 is F_IPIDIHS, ie. improper periodic dihedrals. The switch statement in src/kernel/convparm.c neglects to treat F_IPIDIHS, hence the error. I've noted in the past that the implementation of F_IPIDIHS seems not quite right - see http://lists.gromacs.org/pipermail/gmx-users/2010-August/053262.html. Looking back through time with "git blame", the implementation of these functions was partially done in 2002 and apparently never finished properly. I'd lodge a Bugzilla, but we're in limbo until its replacement is declared available. Meanwhile, you can work around the issue by using the corresponding periodic normal dihedral - the energy breakdown of proper and improper dihedrals reported by mdrun and g_energy won't be correct, however. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] so difficult problem
Dear Amit I entered these commands for rotating box: editconf -f conf.gro -o output.pdb -rotate 0 0 25.4 and then: editconf -f output.pdb -o newbox.pdb -rotate 0 127.67548 0 as a result my molecul is located out of box totally,of course drug and protein are bind to eachother yet. thanks in advance for your attention and reply On Tue, Jan 4, 2011 at 1:25 PM, Amit Choubey wrote: > Could you post the exact command lines ? > > On Tue, Jan 4, 2011 at 1:38 AM, mohsen ramezanpour < > ramezanpour.moh...@gmail.com> wrote: > >> please let me know more. >> I am new with gromacs. >> did I understand correctly?You say me to use from trjconv at first and >> then from editconf? >> I want to keep fix my molecule and rotate my box to locate in awanted >> direction. >> waht can I do? >> because when I rotate the box my molecule totally is located out of >> box,but protein and ligand are connected as the first state and I think my >> molecule has not broken. >> Thanks in advance >> >> >> On Tue, Jan 4, 2011 at 12:56 PM, Amit Choubey wrote: >> >>> May be you broke the molecule while using editconf. Try to fix the >>> periodicity by trjconv and then use it. >>> >>> >>> On Tue, Jan 4, 2011 at 1:14 AM, mohsen ramezanpour < >>> ramezanpour.moh...@gmail.com> wrote: >>> I generated my .top and .gro file as drug/enzyme tutorial. I used PRODRG to generate them. I could pass all of steps in UMbrella sampling tutorial with these files,without any warning or error. the one thing I changed is rotating box with editconf. On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey wrote: > There is something wrong with your initial configuration. May be you > forgot to take care of periodicity, how did you get your initial > configuration? Also notice that these kind of problems have been discussed > previously. > > Amit > > On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour < > ramezanpour.moh...@gmail.com> wrote: > >> Dear All >> I am using this .mdp file and I recived the below warnings,I can't >> solve that. >> >> >> title= NPT >> define = >> integrator = md >> tinit= 0 >> dt = 0.002 >> nsteps = 50 >> nstcomm = 1 >> comm-grps= protein non-protein >> niter= 20 >> nstxout = 5000 >> nstvout = 5000 >> nstfout = 0 >> nstlog = 5000 >> nstenergy= 250 >> nstxtcout= 250 >> xtc-precision= 1000 >> xtc_grps = protein non-protein >> energygrps = Protein non-protein >> nstlist = 5 >> ns_type = grid >> pbc = xyz >> rlist= 1.4 >> domain-decomposition = no >> coulombtype = PME >> rcoulomb-switch = 0 >> rcoulomb = 1.4 >> epsilon-r= 1 >> vdw-type = Cut-off >> rvdw-switch = 0 >> rvdw = 1.4 >> DispCorr = EnerPres >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order= 4 >> ewald_rtol = 1e-05 >> epsilon_surface = 0 >> optimize_fft = no >> tcoupl = Nose-hoover >> tc-grps = Protein non-protein >> tau_t= 0.1 0.1 >> ref_t= 300 300 >> Pcoupl = Parrinello-Rahman >> Pcoupltype = Isotropic >> tau_p= 1.0 >> compressibility = 4.5e-5 >> ref_p= 1.0 >> annealing= no >> gen_vel = yes >> gen_temp = 310 >> gen_seed = 173529 >> constraints = all-bonds >> constraint-algorithm = Lincs >> unconstrained-start = no >> lincs-order = 4 >> lincs-warnangle = 30 >> morse= no >> >> my sytem is protein-ligand,I want to generate a NPT. >> the result was: >> >> Step 0, time 0 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 0.002537, max 0.119994 (between atoms 5293 and 5294) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> starting mdrun 'Protein in water' >> 50 steps, 1000.0 ps. >> >> Step 0, time 0 (ps) LINCS WARNING >> relative constraint deviation after LINCS:
Re: [gmx-users] so difficult problem
Hi Mohsen, I think rotating a molecule with editconf will not rotate the box. Then again, if it did, it would result in a box violating Gromacs requirements. Either way, it's not going to work like that. Build a new box after rotation... And have a good look at what you're actually trying now by taking the rotated system and stack it a few times using genconf -nbox 2 2 2 Cheers, Tsjerk On Jan 6, 2011 7:22 PM, "mohsen ramezanpour" wrote: Dear Amit I entered these commands for rotating box: editconf -f conf.gro -o output.pdb -rotate 0 0 25.4 and then: editconf -f output.pdb -o newbox.pdb -rotate 0 127.67548 0 as a result my molecul is located out of box totally,of course drug and protein are bind to eachother yet. thanks in advance for your attention and reply On Tue, Jan 4, 2011 at 1:25 PM, Amit Choubey wrote: > > Could you post the e... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] methanol simulation
Dear Mark, so, what should I do? mustafa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] methanol simulation
mustafa bilsel wrote: Dear Mark, so, what should I do? In the future, it would be helpful to reply to the original thread instead of starting a new one. You said you added a line "SOL 291" to your [molecules] directive. That would imply that you named your methanol [moleculetype] SOL. If this is not the case, then you're providing an invalid name, and hence the fatal error. -Justin mustafa -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] methanol simulation error
Hi all, I try to make a simulation in methanol. I use gromos43a1 forcefield. My command follow, pdb2gmx -f xxx.pdb editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro When grompp for minimization it gives an error: Atomtype CMET not found I have used grep to count the methanol molecules and added SOL 660 comment in .top file to tell the number of methanols. Also I added #include "gromos43a1.ff/methanol.itp" line to .top. Please don't suggest non-water solvation in how-to part of Gromacs web. Could you tell me what missing is? best wishes mustafa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] methanol simulation error
Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, January 10, 2011. For all questions about CloudBroker, please contact the company under i...@cloudbroker.com. In case you have any issues with the CloudBroker Platform, please send an email to our helpdesk at platf...@cloudbroker.com. If you need to talk to me in person for urgent or important issues, please call my mobile phone number. Kind regards, Wibke Sudholt -- Dr. Wibke Sudholt Associate and Chair of the Management CloudBroker GmbH Technoparkstrasse 1 CH-8005 Zurich Switzerland Phone: +41 44 633 79 34 Email: i...@cloudbroker.com Web:http://www.cloudbroker.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] methanol simulation error
mustafa bilsel wrote: Hi all, I try to make a simulation in methanol. I use gromos43a1 forcefield. My command follow, pdb2gmx -f xxx.pdb editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro When grompp for minimization it gives an error: Atomtype CMET not found I will assume you're not using the current version of Gromacs. This was a bug that was fixed some time ago. Please upgrade to version 4.5.3. I have used grep to count the methanol molecules and added SOL 660 comment in .top file to tell the number of methanols. Is SOL the appropriate name given in the [moleculetype] directive for methanol? The name "SOL" is the default name for water in Gromacs, so this may be where you're having problems. Just because methanol is a solvent doesn't mean it should be named SOL. Check the name in the topology to be sure this is what you should be using. -Justin Also I added #include "gromos43a1.ff/methanol.itp" line to .top. Please don't suggest non-water solvation in how-to part of Gromacs web. Could you tell me what missing is? best wishes mustafa -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] methanol simulation error
On 7/01/2011 12:31 PM, mustafa bilsel wrote: Hi all, I try to make a simulation in methanol. I use gromos43a1 forcefield. My command follow, pdb2gmx -f xxx.pdb editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro When grompp for minimization it gives an error: Atomtype CMET not found I have used grep to count the methanol molecules and added SOL 660 comment in .top file to tell the number of methanols. Also I added #include "gromos43a1.ff/methanol.itp" line to .top. I'm not sure why I'm repeating myself, but the name given in that moleculetype is not SOL. That name must match what appears in the [molecules] section. Please make sure you have read the examples in Chapter 5 of the manual and understand everything there. Please don't suggest non-water solvation in how-to part of Gromacs web. Could you tell me what missing is? You're using atomtype CMET somewhere in your .top or its #included .itp files. Your forcefield doesn't define atomtype CMET, and it needs to if your usage is correct. Without seeing your topology, we can't say more. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] methanol simulation error
Please copy and paste in here the contents of your .top file. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mustafa bilsel Sent: Friday, 7 January 2011 12:32 PM To: gmx-users@gromacs.org Subject: [gmx-users] methanol simulation error Hi all, I try to make a simulation in methanol. I use gromos43a1 forcefield. My command follow, pdb2gmx -f xxx.pdb editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro When grompp for minimization it gives an error: Atomtype CMET not found I have used grep to count the methanol molecules and added SOL 660 comment in .top file to tell the number of methanols. Also I added #include "gromos43a1.ff/methanol.itp" line to .top. Please don't suggest non-water solvation in how-to part of Gromacs web. Could you tell me what missing is? best wishes mustafa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] trjconv with multiple chains problem
dear all, I am doing a simulation that have many chains in a box , and I can find a center for them after serval tries. I use almost every option of trjconv,-pbc mol,atom,res,whole,nojump , -ur compact, -center , -box to got bigger box, and -boxcenter, -fit .. still some chain cannot convert into box. them jump from one box to another , is there any ways that they not jump to another box? thanks a lot. yuanyuan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv with multiple chains problem
yuanyuan wang wrote: dear all, I am doing a simulation that have many chains in a box , and I can find a center for them after serval tries. I use almost every option of trjconv,-pbc mol,atom,res,whole,nojump , -ur compact, -center , -box to got bigger box, and -boxcenter, -fit .. still some chain cannot convert into box. them jump from one box to another , is there any ways that they not jump to another box? thanks a lot. Use a custom index group to center on some subset of atoms that you want to be centered in the system. If you try to just center on, for example, "Protein," the geometric center may lie in the middle of the unit cell but the chains are split across periodic boundaries. -Justin yuanyuan -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] trjconv with multiple chains
dear all, I am doing a simulation that have many chains in a box , and I can find a center for them after serval tries. I use almost every option of trjconv,-pbc mol,atom,res,whole,nojump , -ur compact, -center , -box to got bigger box, and -boxcenter, -fit .. still some chain cannot convert into box. them jump from one box to another , is there any ways that they not jump to another box? thanks a lot. yuanyuan-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
