Hi, Is it possible in GROMACS to extract from trajectory file 9 components of tensor of inertia moments at each time step? I know that it is possible to extract 3 vectors, but not whole tensor. Any suggestions?
Thank you Egis --- On Tue, 12/1/09, [email protected] <[email protected]> wrote: > From: [email protected] <[email protected]> > Subject: gmx-users Digest, Vol 67, Issue 153 > To: [email protected] > Date: Tuesday, December 1, 2009, 12:43 AM > Send gmx-users mailing list > submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' > to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more > specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: Tabulated potentials make newbies > crazy (Mark Abraham) > 2. Re: Fwd: Last step before CG em.mdp > (Francesco Pietra) > 3. Re: Problem with output structures > generated by energy > minimization with GROMACS 4 (HAO > JIANG) > 4. Re: Fwd: Last step before CG em.mdp > (Justin A. Lemkul) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 01 Dec 2009 07:44:51 +1100 > From: Mark Abraham <[email protected]> > Subject: Re: [gmx-users] Tabulated potentials make newbies > crazy > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > ms wrote: > > Mark Abraham ha scritto: > > > Sorry, I was a bit incomplete last night. > Charge groups are the > >> fundamental unit for neighbour-searching (3.4.2) > to construct lists of > >> charge groups for nonbonded interactions, which > determine lists of > >> atom-atom interactions. However, the nonbonded > interactions are > >> evaluated as nested sums, first over energy > groups. So for energy groups > >> of Protein and SOL, the neighbour search finds all > pairs of charge > >> groups that are both Protein and inside the > cutoffs, and lists them. > >> Then all Protein-SOL similarly, then all SOL-SOL. > This requires that the > >> energy groups be a union of only complete charge > groups (and I am not > >> aware that this is spelled out anywhere in the > manual!). So for energy > >> groups of Calpha, Rest_of_Protein and SOL, it > would be necessary to use > >> an individual charge group for each Calpha. This > would usually mean it > >> has a net non-integral charge that is equal in > magnitude of the charge > >> of the group from which it is taken. It is well > known that small charge > >> groups of non-integral charge can then wander back > and forth across > >> cut-off boundaries and generate artefacts. > > > > Ok, thanks for the clarification. This doesn't suggest > a trivial > > solution to the problem, quite the opposite: I > understood correctly that > > charge groups must be neutral, and this is impossible > to do if we put > > each C-alpha as a charge group. > > > > I can coarse the thing further -that's quite the plan, > actually- and > > eliminate electrostatics, but I hoped to have a look > at what happens > > with the new potential and getting it right, before > going so far. > > > > So, even if the following: > >>> The problem is that since I have a single > molecule now, and the single > >>> molecule must be neutral, so it must be all a > single charge group > >>> ("Therefore we have to keep groups of atoms > with total charge 0 > >>> together. These groups are called charge > groups.", 4.6.2). > > > > is not entirely correct, it is indeed correct that > charge groups > > *should* be neutral. Isn't it? > > Indeed. See 3.4.2 and ref therein. > > >> If you're running in single precision, that > precision cannot represent > >> values as large as 10^41. Since in any simulation > (but particularly > >> coarse-grained one) non-bonded atoms aren't going > to get this close, the > >> values are next to irrelevant. Just choose 10^38 > for anything larger > >> than that. > > > > Right, it is probably precision problem. Thanks. > > > >>>>> Now, my questions are: > >>>>> - What is the accepted range of values > in tables? > >>>> I don't think this is the problem. > >>> It is the least problem probably, given my > confusion on energy-charge > >>> groups, but it seems it is too... > >>> > >>>>> - How do I define a steep repulsion > potential correctly? > >>>> It's terse, but manual 6.7 seems to have > the necessary information. > >>> 6.7 is one of the references I am obviously > using, but it gives only > >>> general (even if essential!!) information, > nothing speficic on "good" or > >>> "bad" potential shapes/values. But probably > that's the least problem :) > >> Knowing a sensible shape is your problem, if > you're choosing to > >> unbalance the force field by changing one of the > contributing potentials... > > > > I meant "sensible" in the meaning of "can be > interpolated more or less > > faithfully / will be calculated with more or less > artefacts" -of course > > if it makes sense in the model is my problem... > > The cubic spline interpolation will do a mighty fine job of > any function > that is suitably continuous provided that the density of > points is > sufficiently fine... interpolating a sinusoid with a > density comparable > with the period would obviously be a disaster! > > Mark > > > ------------------------------ > > Message: 2 > Date: Mon, 30 Nov 2009 21:49:13 +0100 > From: Francesco Pietra <[email protected]> > Subject: Re: [gmx-users] Fwd: Last step before CG em.mdp > To: [email protected], > Discussion list for GROMACS users > <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=UTF-8 > > On Mon, Nov 30, 2009 at 8:18 PM, Justin A. Lemkul <[email protected]> > wrote: > > > > > > Francesco Pietra wrote: > >> > >> Failed to specify that both the DPPC bilayer and > the box of water are > >> from equilibrated systems in MARTIN web, while the > protein was Amber > >> minimized (and MD) before generating the CG. > >> > >> I have tried the cg protein alone > >> > >> genbox -cp my.pdb -box 15 -o my.gro > >> > > > > Again I ask why you are using SPC as the solvent. If > you indeed want to use > > the MARTINI CG water representation, you must pass its > configuration > > explicitly to the -cs flag. Otherwise, the default > (spc216.gro) is used. > > The water that I set around the extracellular part of the > protein was > equilibrated cg water (by just multiplying the box > furnished on > MARTINI). In relation to the command above, I don't > understand your > remark, simply because there is no water at all, both in > the input > .pdb and output.gro. This is true for my previous post, > too. > > > > > > Are you defining the protein's position in the box > before solvation? Using > > editconf -c is your friend. > > I did present work before getting your mail. Curiously, > gmail now > places your mail in spam. Luckily I noticed that. > A point I have to pay much attention to - for a possible > major mistake > in my procedure - is your "before solvation". I assumed no > solvation > at all. > > > > > > >> grompp -f em.mdp -c my.gro -p my.top -o topol.tpr > >> > >> mdrun -v -s topol.tpr > >> > >> steepest descents converged to machine precision > but not to the > >> requested Fmax < 2000 > >> > >> Pot Ener 7.1e+08 > >> Max force 6.1e+10 on atom 983 > >> Norm of force 2.5e+11 > >> > >> confout.gro shows that one of the subunits has > been displaced from the > >> multimer (apparently both intact) There is a long > bond between the > >> displaced subunit and the rest of the multimer, > very closely to the > >> atom 983 of max force, located in the pore region. > I have scarce > >> experience with gromacs yet, hope that this > suggests remedies. I used > >> a crude version of em.mdp. > >> > > > > Well, there are several potential problems. One is > the box size (as I > > mentioned in my last message). The other question is > whether or not the > > conversion from atomistic to CG was done correctly. > I know I have mentioned > > the problems with the MARTINI script a number of > times, and perhaps this has > > also come up in our discussions before, but do check > that the starting CG > > coordinates make sense. > > The cg protein model superimposes nicely to the full-atom > model. The > dimensions I gave in my previous mail were DPPC and W > inclusive but > "-box 15" is still to small. The protein might have seen > its neighbor. > > > > > Beyond that, try an in vacuo minimization of your > protein and see what > > happens there. > > Do you mean without setting "-box"? I got confused about > that, I > thought to have vacum around the protein (or the > protein+DPPC+W of > previous mail) with > > genbox -cp my.pdb -box 15 -o my.gro > > > I'll try tomorrow to implement all your suggestions. Thanks > a lot > francesco > > > > > -Justin > > > > -- > > ======================================== > > > > 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 list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. > Use the www interface > > or send it to [email protected]. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > ------------------------------ > > Message: 3 > Date: Mon, 30 Nov 2009 15:50:48 -0500 > From: "HAO JIANG" <[email protected]> > Subject: Re: [gmx-users] Problem with output structures > generated by > energy minimization > with GROMACS 4 > To: "Discussion list for GROMACS users" <[email protected]> > Message-ID: > <3774c6b488994877b47fa3d7f3f59...@leihao> > Content-Type: text/plain; > charset="UTF-8" > > Tsjerk, > > Thanks for your reply. > > I am doing a simple test case with 500 SPC/E water > molecules. First I did minimization with steepest decent, > using a command like > > mdrun -pd -s water.gro.tpr -c final.gro > > The generated md.log looks like the following: > ---------------- > Step > Time > Lambda > 0 > 0.00000 > 0.00000 > Energies (kJ/mol) > LJ (SR) Disper. > corr. Coulomb (SR) Coul. > recip. Potential > > 4.70442e+03 -7.34875e+02 -2.65916e+04 -1.28439e+03 -2.39065e+04 > Pressure (bar) > 2.27899e+04 > . > . > . > Step > Time > Lambda > 1000 > 1000.00000 > 0.00000 > Energies (kJ/mol) > LJ (SR) Disper. > corr. Coulomb (SR) Coul. > recip. Potential > > 5.53526e+03 -7.34875e+02 -3.22651e+04 -1.33018e+03 -2.87949e+04 > Pressure (bar) > 2.42765e+04 > > > Steepest Descents did not converge to Fmax < 1 in 1001 > steps. > Potential Energy = -2.87949018657418e+04 > Maximum force = > 6.95206177080918e+01 on atom 1033 > Norm of force = > 3.71165837023948e+00 > -------- > > Just for testing I tried to do further optimization. I > created a new tpr with the generated final.gro file and the > old top and mdp files, then run mdrun again. > > This time the generated md.log looks like the following: > > === > Step > Time > Lambda > 0 > 0.00000 > 0.00000 > Energies (kJ/mol) > LJ (SR) Disper. > corr. Coulomb (SR) Coul. > recip. Potential > > 4.70442e+03 -7.34875e+02 -2.65916e+04 -1.28439e+03 -2.39065e+04 > Pressure (bar) > 2.27899e+04 > > . > . > . > ==== > > So it seems like final.gro has a potential energy that is > very close to that of the original, un-optimized > structure. > > While I repeat the same procedure with Gromacs 3.3, > everything works as expected. For the first optimization I > got > > --- > Step > Time > Lambda > 0 > 0.00000 > 0.00000 > Energies (kJ/mol) > LJ (SR) Disper. > corr. Coulomb (SR) Coul. > recip. Potential > > 4.70486e+03 -7.34875e+02 -2.65916e+04 -1.28441e+03 -2.39060e+04 > Kinetic En. Total > Energy Temperature Pressure (bar) > 0.00000e+00 0.00000e+00 > 0.00000e+00 -1.63608e+03 > . > . > . > Step > Time > Lambda > 999 > 999.00000 0.00000 > > Energies (kJ/mol) > LJ (SR) Disper. > corr. Coulomb (SR) Coul. > recip. Potential > > 5.48610e+03 -7.34875e+02 -3.21894e+04 -1.29343e+03 -2.87316e+04 > Kinetic En. Total > Energy Temperature Pressure (bar) > 0.00000e+00 0.00000e+00 > 0.00000e+00 -1.63608e+06 > > Step > Time > Lambda > 1000 > 1000.00000 > 0.00000 > > > Steepest Descents did not converge to Fmax < 1 in 1001 > steps. > Potential Energy = -2.87316123776041e+04 > Maximum force = > 2.72102300902620e+01 on atom 136 > Norm of force = > 2.08471187918543e+02 > --- > > and for the further optimization I got > > === > Step > Time > Lambda > 0 > 0.00000 > 0.00000 > Energies (kJ/mol) > LJ (SR) Disper. > corr. Coulomb (SR) Coul. > recip. Potential > > 5.48626e+03 -7.34875e+02 -3.21871e+04 -1.29320e+03 -2.87289e+04 > Kinetic En. Total > Energy Temperature Pressure (bar) > 0.00000e+00 0.00000e+00 > 0.00000e+00 -1.63608e+03 > . > . > . > === > > I don't know what causes the difference. > > Hao Jiang > > > > > ----- Original Message ----- > From: "Tsjerk Wassenaar" <[email protected]> > To: "Discussion list for GROMACS users" <[email protected]> > Sent: 2009年11月30日 12:37 PM > Subject: Re: [gmx-users] Problem with output structures > generated by energy minimization with GROMACS 4 > > > Ni Hao, > > You don't give too much information here. What exactly are > you doing? > What are the commands? What's the difference between the > first and the > second pass of EM? One thing to check is whether the > output/input file > has a correct box definition. > > Cheers, > > Tsjerk > > 2009/11/30 HAO JIANG <[email protected]>: > > Hi, > > > > I got a problem with the output structure files > (gro/trr/xtc) generated by > > the energy minimization with GROMACS 4. That is, when > I used the generated > > structure as the input for further minimizations or MD > simulations, I got > > very large potential energy and forces at step 0, as > if the structure had > > not been optimized at all. On the other hand, there is > no problem when > > the input structure is taken from a previous MD run, > and I got the expected > > potential at step 0. There is no problem, too, if I > use GROMACS 3 to do the > > minimization. > > > > Any help is greatly appreciated! > > > > Hao Jiang > > > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. > Use the > > www interface or send it to [email protected]. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > Computational Chemist > Medicinal Chemist > Neuropharmacologist > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use > the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ------------------------------ > > Message: 4 > Date: Mon, 30 Nov 2009 16:43:22 -0500 > From: "Justin A. Lemkul" <[email protected]> > Subject: Re: [gmx-users] Fwd: Last step before CG em.mdp > To: "Gromacs Users' List" <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > Francesco Pietra wrote: > > On Mon, Nov 30, 2009 at 8:18 PM, Justin A. Lemkul > <[email protected]> > wrote: > >> > >> Francesco Pietra wrote: > >>> Failed to specify that both the DPPC bilayer > and the box of water are > >>> from equilibrated systems in MARTIN web, while > the protein was Amber > >>> minimized (and MD) before generating the CG. > >>> > >>> I have tried the cg protein alone > >>> > >>> genbox -cp my.pdb -box 15 -o my.gro > >>> > >> Again I ask why you are using SPC as the > solvent. If you indeed want to use > >> the MARTINI CG water representation, you must pass > its configuration > >> explicitly to the -cs flag. Otherwise, the > default (spc216.gro) is used. > > > > The water that I set around the extracellular part of > the protein was > > equilibrated cg water (by just multiplying the box > furnished on > > MARTINI). In relation to the command above, I don't > understand your > > remark, simply because there is no water at all, both > in the input > > .pdb and output.gro. This is true for my previous > post, too. > > > > Oops, my mistake. I forgot that -cs was optional, and > not taken as default :) > Never mind that comment. > > > > >> Are you defining the protein's position in the box > before solvation? Using > >> editconf -c is your friend. > > > > I did present work before getting your mail. > Curiously, gmail now > > places your mail in spam. Luckily I noticed that. > > A point I have to pay much attention to - for a > possible major mistake > > in my procedure - is your "before solvation". I > assumed no solvation > > at all. > > > > > > > >>> grompp -f em.mdp -c my.gro -p my.top -o > topol.tpr > >>> > >>> mdrun -v -s topol.tpr > >>> > >>> steepest descents converged to machine > precision but not to the > >>> requested Fmax < 2000 > >>> > >>> Pot Ener 7.1e+08 > >>> Max force 6.1e+10 on atom 983 > >>> Norm of force 2.5e+11 > >>> > >>> confout.gro shows that one of the subunits has > been displaced from the > >>> multimer (apparently both intact) There is a > long bond between the > >>> displaced subunit and the rest of the > multimer, very closely to the > >>> atom 983 of max force, located in the pore > region. I have scarce > >>> experience with gromacs yet, hope that this > suggests remedies. I used > >>> a crude version of em.mdp. > >>> > >> Well, there are several potential problems. > One is the box size (as I > >> mentioned in my last message). The other > question is whether or not the > >> conversion from atomistic to CG was done > correctly. I know I have mentioned > >> the problems with the MARTINI script a number of > times, and perhaps this has > >> also come up in our discussions before, but do > check that the starting CG > >> coordinates make sense. > > > > The cg protein model superimposes nicely to the > full-atom model. The > > dimensions I gave in my previous mail were DPPC and W > inclusive but > > "-box 15" is still to small. The protein might have > seen its neighbor. > > > > Then that's certainly the first problem to fix. This > is why I generally use > editconf for defining the box (and why I keep recommending > it). For a simple > protein in water, using a command like: > > editconf -c -d 1.0 > > will define a suitably-sized box so that you don't have to > guess at the box > dimensions. There is no such option with genbox. > > >> Beyond that, try an in vacuo minimization of your > protein and see what > >> happens there. > > > > Do you mean without setting "-box"? I got confused > about that, I > > thought to have vacum around the protein (or the > protein+DPPC+W of > > previous mail) with > > > > You can disregard that comment, I had assumed from reading > the earlier post that > you had solvated the structure. If the protein does > not minimize by itself > (hence, in vacuo) then perhaps your issue comes from your > box dimensions. Seems > most likely at this point. > > I don't think you want a vacuum around your system. > That's the whole point of > PBC is it not - to avoid boundary conditions and "droplet" > formation? What you > want to do is assign a box that actually fits your system > :) > > -Justin > > -- > ======================================== > > 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 list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 67, Issue 153 > ****************************************** > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
