Re: [gmx-users] Dihedral restraints in 4.6 vs 4.5.X
Thanks - I have filed issue #1194 and assigned it to David. http://redmine.gromacs.org/issues/1194 Let me know if there is anything else that is needed. I could take a shot at myself, and will play around with it, but I don't know the details of the symtab in any detail, unfortunately. 15 mar 2013 kl. 19:51 skrev David van der Spoel: Taking away the restraint allows me to start the run in 4.6.1, and also reformatting the [ dihedral_restraint ] section to comply with 4.6 works. Is this a know issue, am I missing something obvious, or should I file an issue on redmine? redmine please. Thanks /Per-- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Dihedral restraints in 4.6 vs 4.5.X
Hi I anyone aware of any issue starting simulations with 4.6 (or 4.6.1) from a 4.5.X-tpr file with dihedral restraints? I'm unsuccessful in making them start. To investigate further, I created a small dialanine peptide in vacuum, with a dihedral restraint. Here's the details: Making a 4.5.5 tpr with a dihedral restraint $grompp -f md.mdp -c conf.gro -p topol.top -o md.tpr Checking that it is there: $gmxdump -s md.tpr |grep DIHRE Reading file md.tpr, VERSION 4.5.5 (single precision) functype[166]=DIHRES, label=0, power= 1 phi= 1.2000e+02, dphi= 3.e+01, kfac= 1.e+00) Now running this in 4.5.5 works fine, but starting it in 4.6 (or 4.6.1) gives me an error. $ /Users/per/source/gromacs-4.6.1/build/src/kernel/mdrun -v -deffnm md Reading file md.tpr, VERSION 4.5.5 (single precision) --- Program mdrun, VERSION 4.6.1 Source code file: /Users/per/source/gromacs-4.6.1/src/gmxlib/symtab.c, line: 136 Fatal error: symtab get_symtab_handle 1051260126 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Taking away the restraint allows me to start the run in 4.6.1, and also reformatting the [ dihedral_restraint ] section to comply with 4.6 works. Is this a know issue, am I missing something obvious, or should I file an issue on redmine? Thanks /Per-- 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] cmaptypes format
Hi Francesco That number corresponds to a type for each cmap-entry. The idea (iirc, it was some time ago) was that it could be useful to be able to have multiple cmap-types (other grid values, different grid spacing etc) for the same cmap-dihedral (much like different torsions etc...), but based on a quick look in the code, the support for that is very limited. It should probably not be touched right now. Cheers /Per 19 feb 2013 kl. 15:43 skrev francesco oteri: Dear gromacs users, I am trying to figure out the meaning of the cmaptypes section in file section. As far as I understood, taking the following entry as example: C NH1 CT1 C NH1 1 24 24\ C NH1 CT1 C = phi H1 CT1 C NH1 = psi 24*24 = dimension of the grid My question is: what does the 1 mean? Best, Francesco -- 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
Re: [gmx-users] comparing gmx GB energy with Amber11
After some investigation, it turns out that this is explained by the differences in input radii for the GB-calculation done by Gromacs and Amber. The radii in the gbsa.itp-file are not the same as the ones used by Amber. If one changes the radii in gbsa.itp, you get a difference in 0-step energy (at least for the system below) of 0.2 kJ/mol, which is tolerable. I have pasted a copy of the gbsa.itp-file below, in case it is useful for someone. This was tested with amber99sb. Cheers /Per [ implicit_genborn_params ] ; atype sar st pi gbr hct ;Br 0.1 1 10.125 0.85 ; H C0.1721 1.5540.170.72 ; C CA 0.18 1 1.0370.170.72 ; C CB 0.1720.012 1.5540.170.72 ; C CC 0.1721 1.5540.170.72 ; C CN 0.1720.012 1.5540.170.72 ; C CR 0.18 1 1.0730.170.72 ; C CT 0.18 1 1.2760.17 0.72 ; C CV 0.18 1 1.0730.170.72 ; C CW 0.18 1 1.0730.170.72 ; C C* 0.1720.012 1.5540.170.72 ; C H0.1 1 10.13 0.85 ; H HC 0.1 1 10.12 0.85 ; H H1 0.1 1 10.12 0.85 ; H HA 0.1 1 10.12 0.85 ; H H4 0.1 1 10.12 0.85 ; H H5 0.1 1 10.12 0.85 ; H HO 0.1 1 10.12 0.85 ; H HS 0.1 1 10.12 0.85 ; H HP 0.1 1 10.12 0.85 ; H N0.1551 1.0280.155 0.79 ; N NA 0.1551 1.0280.155 0.79 ; N NB 0.1551 1.2150.155 0.79 ; N N2 0.16 1 1.2150.155 0.79 ; N N3 0.16 1 1.2150.1550.79 ; N O0.15 1 0.9260.15 0.85 ; O OH 0.1521 1.0800.150.85 ; O O2 0.17 1 0.9220.15 0.85 ; O S0.18 1 1.1210.180.96 ; S SH 0.18 1 1.1210.180.96 ; S ; masscenters for vsites do not have gbsa parameters MNH3 00 00 0 MCH3 00 00 0 8 nov 2012 kl. 23:42 skrev Sandeep Somani: Hi Per I tried with single precision gmx as well. No change. Will send you input files soon. Best Sandeep On Thu, Nov 8, 2012 at 3:55 PM, Per Larsson per.lars...@sbc.su.se wrote: Hi Thanks for doing those test. They are all reassuring, I think. Could you maybe send me your input-files off list and I'll take a look. I suspect the issue is that different radii are being used, as Gromacs does not use the Bondi radii. Cheers /Per 8 nov 2012 kl. 16:35 skrev Sandeep Somani: Hi Per Pls see inline comments: 1. If I recall correctly, the GB-energy in gromacs is split into two parts, GB-polarization and non-polar solvation. Can you check whether this is the case and if the value you report is the sum of those two terms. Yes, gromacs prints out GB Polarization and Nonpolar Sol. corresponding to EGB and ESURF, respectively, from Amber. Right now I am just comparing EGB part (non polar also do not match but since it is a much smaller contribution, will worry about that later!). 2. Try setting all cut-offs to 0 (infinite cutoffs). That will trigger a slightly different part of the code to do the GB-calculation (you should see in your log file references to all-vs-all kernels) Just tried -- no change. (btw, i didnt know 0 = no-cutoff. thnx!) 3. Try running in single precision, keeping in mind 1 and 2 above to see if that helps. Also, try setting the GMX_NOOPTIMIZEDKERNELS variable to 1 (at least it used to be called that, someone else can perhaps correct me if that has changed). This will make the code run without the sse-loops. I'll try shortly. 4. It could be that you are using different radii for the atoms in your system. For amber, are you using the Bondi-radii or something else? I tried both set default PBradii mbondi and set default PBradii mbondi2 while creating amber prmtop files in leap. The difference in EGB is just 2-3 kcal/mol .. not enough to bridge the gap. Best Sandeep Cheers /Per 8 nov 2012 kl. 05:43 skrev Sandeep Somani: Hi, I am comparing single point amber ff energies from gmx4.5.5 (double precision) and Amber11. All bonded and non-bonded energy terms are in very good agreement (within 0.1 kJ/mol) except GB: gmx 'GB polarization' = -200 kJ/mol amber 11 'EGB' = -283 kJ/mol. I am basically trying to replicate Amber's igb=5 + large cutoff in gmx. According to Amber manual igb=5 corresponds to model 2 of [2004 OBC paper]. I translated
Re: [gmx-users] comparing gmx GB energy with Amber11
Hi
A few things:
1. If I recall correctly, the GB-energy in gromacs is split into two parts,
GB-polarization and non-polar solvation. Can you check whether this is the case
and if the value you report is the sum of those two terms.
2. Try setting all cut-offs to 0 (infinite cutoffs). That will trigger a
slightly different part of the code to do the GB-calculation (you should see in
your log file references to all-vs-all kernels)
3. Try running in single precision, keeping in mind 1 and 2 above to see if
that helps. Also, try setting the GMX_NOOPTIMIZEDKERNELS variable to 1 (at
least it used to be called that, someone else can perhaps correct me if that
has changed). This will make the code run without the sse-loops.
4. It could be that you are using different radii for the atoms in your system.
For amber, are you using the Bondi-radii or something else?
Cheers
/Per
8 nov 2012 kl. 05:43 skrev Sandeep Somani:
Hi,
I am comparing single point amber ff energies from gmx4.5.5 (double
precision) and Amber11.
All bonded and non-bonded energy terms are in very good agreement (within
0.1 kJ/mol) except GB:
gmx 'GB polarization' = -200 kJ/mol
amber 11 'EGB' = -283 kJ/mol.
I am basically trying to replicate Amber's igb=5 + large cutoff in gmx.
According to Amber manual igb=5 corresponds to model 2 of [2004 OBC
paper].
I translated this to the following mdp options:
implicit_solvent= GBSA
gb_algorithm= OBC
All cut-offs (rcoulomb, rvdw, rlist, rgbradii) larger than the size of the
molecule.
{gb_epsilon_solvent, gb_saltconc, gb_obc_alpha, gb_obc_beta, gb_obc_gamma,
gb_dielectric_offset} = corresponding Amber input.
Is that correct?
I realize that this is as much a question for Amber mailing list, but
trying here first! Any idea?
The molecule is ala-12. I'll be happy to send input files.
Thanks in advance
Sandeep
--
Postdoc
Wales Group
Cambridge
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Re: [gmx-users] comparing gmx GB energy with Amber11
Hi
Thanks for doing those test. They are all reassuring, I think.
Could you maybe send me your input-files off list and I'll take a look.
I suspect the issue is that different radii are being used, as Gromacs does not
use the Bondi radii.
Cheers
/Per
8 nov 2012 kl. 16:35 skrev Sandeep Somani:
Hi Per
Pls see inline comments:
1. If I recall correctly, the GB-energy in gromacs is split into two
parts, GB-polarization and non-polar solvation. Can you check whether this
is the case and if the value you report is the sum of those two terms.
Yes, gromacs prints out GB Polarization and Nonpolar Sol.
corresponding to EGB and ESURF, respectively, from Amber.
Right now I am just comparing EGB part (non polar also do not match but
since it is a much smaller contribution, will worry about that later!).
2. Try setting all cut-offs to 0 (infinite cutoffs). That will trigger a
slightly different part of the code to do the GB-calculation (you should
see in your log file references to all-vs-all kernels)
Just tried -- no change.
(btw, i didnt know 0 = no-cutoff. thnx!)
3. Try running in single precision, keeping in mind 1 and 2 above to see
if that helps. Also, try setting the GMX_NOOPTIMIZEDKERNELS variable to 1
(at least it used to be called that, someone else can perhaps correct me if
that has changed). This will make the code run without the sse-loops.
I'll try shortly.
4. It could be that you are using different radii for the atoms in your
system. For amber, are you using the Bondi-radii or something else?
I tried both set default PBradii mbondi and set default PBradii
mbondi2 while creating amber prmtop files in leap. The difference in EGB
is just 2-3 kcal/mol .. not enough to bridge the gap.
Best
Sandeep
Cheers
/Per
8 nov 2012 kl. 05:43 skrev Sandeep Somani:
Hi,
I am comparing single point amber ff energies from gmx4.5.5 (double
precision) and Amber11.
All bonded and non-bonded energy terms are in very good agreement (within
0.1 kJ/mol) except GB:
gmx 'GB polarization' = -200 kJ/mol
amber 11 'EGB' = -283 kJ/mol.
I am basically trying to replicate Amber's igb=5 + large cutoff in gmx.
According to Amber manual igb=5 corresponds to model 2 of [2004 OBC
paper].
I translated this to the following mdp options:
implicit_solvent= GBSA
gb_algorithm= OBC
All cut-offs (rcoulomb, rvdw, rlist, rgbradii) larger than the size of
the
molecule.
{gb_epsilon_solvent, gb_saltconc, gb_obc_alpha, gb_obc_beta,
gb_obc_gamma,
gb_dielectric_offset} = corresponding Amber input.
Is that correct?
I realize that this is as much a question for Amber mailing list, but
trying here first! Any idea?
The molecule is ala-12. I'll be happy to send input files.
Thanks in advance
Sandeep
--
Postdoc
Wales Group
Cambridge
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Hi
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Re: [gmx-users] MM/PBSA Gromacs
Hi! There is support in gromacs for gb calculations. However, I'm currently investigating some recent reports about unstable simulations (unfolding proteins), so my advice is to use the code with caution. Thanks /Per 30 nov 2011 kl. 20:04 skrev R.S.K.Vijayan biovija...@gmail.com: Dear Gromacs users Is there any script that does a PB or GB calculation to perform a MM/PB(GB)SA free energy calculation in Gromacs. Similar to the MMPBSA.py script available in Amber. I find a similar question raised by a user a couple of years back. Any successful implementation Vijayan.R On Wed, Nov 30, 2011 at 1:26 PM, Justin A. Lemkul jalem...@vt.edu wrote: 김현식 wrote: Dear Experts, Hi, Is there any tools in gromacs to get Hydrophobic cores of protein ? I suppose that depends on what your definition is, but in all likelihood no, not directly. A program like g_sas can give you nonpolar and polar surface areas as well as volumes and surface atoms, which, through crafty use of index groups, may provide you with something useful. -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 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
Re: [gmx-users] System heating up during MD run? (Implicit solvent)
Hi There has been a number of reports lately about ill-behaving simulations using implicit solvent. I'm currently trying to investigate the cause of this, as such simulations used to work very nice in our hands. In the meantime I would advice to use implicit solvent with caution. Thanks /Per Skickat från min iPhone 30 okt 2011 kl. 02:10 skrev Matt Larson larsonma...@gmail.com: I've been having problems getting implicit solvent systems (which are probably fairly experiment still in gromacs) to work correctly. I've been modelling a protein of about 11000 atoms with hydrogens in a 2 ns simulation. By the end of the simulation, the temperature has risen from 300 K to 496 K - and the protein unfolds. It was supposed to maintain temp at 300 K. I have an a non-zero total charge of -6.99. With explicit solvent, I would normally add the appropriate matching ions, but with implicit solvent what should you do? Could the non-zero total charge result in heating? Or is the thermostat not working well enough (should I change tau-t or ref-t?) Here is my md.mdp file: constraints = all-bonds ; trying.. integrator = md dt = 0.002; ps ! nsteps = 100 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = cut-off fourierspacing = 0.16 vdwtype = cut-off rcoulomb= 1.0 rvdw= 1.0 ; important for neighbor searching pbc = no ; no periodic boundary conditions epsilon_rf = 0 rgbradii= 1.0 ; must equal rlist, rcoulomb, rvdw comm_mode = angular optimize_fft= yes implicit_solvent= GBSA gb_algorithm= OBC gb_epsilon_solvent = 80 sa_surface_tension = 2.25936 nstcomm = 10 nstxout = 1000 nstxtcout = 1000 nstvout = 0 nstfout = 0 tcoupl = andersen tc-grps = system tau-t = 0.1 ref-t = 300 gen_vel = yes gen_temp= 300 gen_seed= -1 - -- 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
Re: [gmx-users] Energy Drift
Hi Justin! Do you maybe have an example of such a protein (preferably not too large :-), that I could run some tests on? I'd be interested in seeing if there has been any bugs introduced in the cutoff code that destabilises proteins that way. Thanks /Per 18 okt 2011 kl. 23:41 skrev Justin A. Lemkul jalem...@vt.edu: Ben Reynwar wrote: I posted to the list a few days ago with an energy drift problem. Mark Abraham helpfully suggested using all-bonds rather than h-bonds which solved the problem. I'm now trying to understand quite why that helped so much. The simulation is a protein of about 5000 atoms using GBSA, a time step of 2 fs, and a cut-off of 1.6 for VdW, coulomb and GB. I've run energy drift simulations using the md integrator, with no thermostat, and using the ld integrator with a tau_t of 100. Simulations were run changing various parameters. The changes were: - dt reduced to 1.5 - dt reduced to 1.0 - cutoff increased to 2.0 - constraint changed from h-bonds to all-bonds Plot of the energy drifts can be seen at http://www.reynwar.net/ben/gromacs/energy_drift.png. Noticeable features are: - changing the time step makes no difference (in my last post I claimed it did, which is why you should make plots rather than eyeballing log files). - increasing the cut-off helps a lot. - changing constraint to all-bonds make a dramatic difference - using ld there is a downwards drift in the energy when using all-bonds constraint. The temperature is roughly 300 K and the set point is 400 K so this downwards drift seems unlikely to be due to coupling to the langevin thermostat. My questions are: - why does the all-bonds constraint help so much? - why doesn't moving to a smaller time step help with this? - what is the cause of the downwards drift when using ld with all-bonds? I can offer a bit of general advice here, but no specific answers. Hopefully it helps. To get at the root cause of all of this, you should be analyzing individual energy components, not just the total energy. These will tell you which terms are systematically changing. In my experience with GB simulations, using anything other than infinite cutoffs (i.e. all-vs-all kernel) has resulted in unstable simulations. I don't mean that the simulations crash or anything, but the results are clearly incorrect. Stably folded proteins have drastically increased RMSD and lose their structure very easily. The effect is independent of the chosen force field. I would recommend always using infinite cutoffs for GB simulations. It may improve your situation. -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 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
Re: [gmx-users] Simulation runs on iMac but explodes on cluster
Hi! Could you try running with GMX_NOOPTIMIZEDKERNELS=1, to see if this could potentially be a bug in the sse code (I noticed nb_kernel410_x86_64_sse in your error message. Thanks /Per 13 jul 2011 kl. 09.35 skrev Luke Goodsell: As the subject suggests, I have a simulation that runs correctly on my iMac, but fails when I try to run it on a cluster, and I am hoping someone may be able to suggest which things to try first to resolve the issue. -- 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] Questions about GB parameters
Hi! Yes, I did! Had to look up a conversation between me and the Tinker developers about precisely this. The values are indeed not the original ones, but rather developed internally by Tinker people so to minimise differences between analytical surface areas and GB, given the HCT-algorithm and using per-atom rather than per-pair scale factors. The values have not been published anywhere as such but have been used by others and seem fairly robust, according to Tinker developers. In the light of all other approximations introduced with implicit solvent, the differences in results should be minor. Of course this needs to be properly documented, and it was very good that some light was shed on this. /Per 6 jul 2011 kl. 04:29 skrev Justin A. Lemkul jalem...@vt.edu: Per Larsson wrote: Hi! I did some digging and think I can clarify at least the first question. Sorry for the confusion with regard to the earlier post. What is specified in the gbsa.itp file under the gbr column is indeed vdW-radii. These are used to compute Born radii, as the manual says. The dielectric offset is subtracted from the vdW radii, as this has been shown to improve the agreement between PB and GB calculations (see eg. the OBC-paper, Onufriev, Bashford and Case, Proteins, 55, 383-394). For the second question, I am a little confused myself now. The values found in the gbsa.itp-file are exactly those found in the Tinker package (in the ksolv.f-routine), which also cites the same reference. Hmm...I'll be back again for this one. Have you uncovered anything? I've tried contacting the Tinker developers but have received no response. I found the routine (in Tinker's born.f) that utilizes the values, but I still have no idea where they come from or why they're fixed for a given atom type rather than a given pair. -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 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
Re: [gmx-users] Questions about GB parameters
Hi! I did some digging and think I can clarify at least the first question. Sorry for the confusion with regard to the earlier post. What is specified in the gbsa.itp file under the gbr column is indeed vdW-radii. These are used to compute Born radii, as the manual says. The dielectric offset is subtracted from the vdW radii, as this has been shown to improve the agreement between PB and GB calculations (see eg. the OBC-paper, Onufriev, Bashford and Case, Proteins, 55, 383-394). For the second question, I am a little confused myself now. The values found in the gbsa.itp-file are exactly those found in the Tinker package (in the ksolv.f-routine), which also cites the same reference. Hmm...I'll be back again for this one. Cheers /Per 21 jun 2011 kl. 18.42 skrev Justin A. Lemkul: Can anyone comment further on either of these issues? -Justin Mark Abraham wrote: On 15/06/2011 4:24 AM, Justin A. Lemkul wrote: Hi All, I wanted to dig up an old discussion that hit the list a long time ago because I'm now encountering some problems understanding the GB settings myself. The discussion in question is here: http://lists.gromacs.org/pipermail/gmx-users/2010-August/053373.html I wanted to post a couple of questions based on Per's response. 1. Based on that post, it seems to me that the value in the gbr column should have a dielectric offset added to it during the GB calculations. In the code, though (genborn.c, around line 484 in the latest release-4-5-patches), it looks like the dielectric offset is subtracted, not added. I guess the code is reversing the process, going from GB radius back to vdW radius by subtracting the dielectric offset? It seems, then, that the parameters in gbsa.itp should specify GB radii, not vdW radii, though the manual says the gbr column is atomic van der Waals radii, which are used in computing the Born radii. Is the opposite actually true? It does look to me as though something is mis-sense here. The quantity given in gb_dielectric_offset is always subtracted from a value that I think is found in the gbr column of [implicit_genborn_parameters]. Mark 2. I am still unclear on the source of the HCT scaling factors. From the reference cited in the manual, it would seem that scaling factors are interaction-dependent, at least when H atoms are concerned. I also cannot find any indication of where these values came from. None of the values of Table 2 in the HCT reference match the contents of the hct column. Again I wonder if I'm missing something obvious :) Thanks for any insight! -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 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
Re: [gmx-users] Questions about GB parameters
Hi! Hmm.. Let me see if I can shed some more light on this. It's been a while though since I visited the literature here, and also my laptop broke down today, so I need to take of that first before I can check the code! Thanks /Per 14 jun 2011 kl. 20:24 skrev Justin A. Lemkul jalem...@vt.edu: Hi All, I wanted to dig up an old discussion that hit the list a long time ago because I'm now encountering some problems understanding the GB settings myself. The discussion in question is here: http://lists.gromacs.org/pipermail/gmx-users/2010-August/053373.html I wanted to post a couple of questions based on Per's response. 1. Based on that post, it seems to me that the value in the gbr column should have a dielectric offset added to it during the GB calculations. In the code, though (genborn.c, around line 484 in the latest release-4-5-patches), it looks like the dielectric offset is subtracted, not added. I guess the code is reversing the process, going from GB radius back to vdW radius by subtracting the dielectric offset? It seems, then, that the parameters in gbsa.itp should specify GB radii, not vdW radii, though the manual says the gbr column is atomic van der Waals radii, which are used in computing the Born radii. Is the opposite actually true? 2. I am still unclear on the source of the HCT scaling factors. From the reference cited in the manual, it would seem that scaling factors are interaction-dependent, at least when H atoms are concerned. I also cannot find any indication of where these values came from. None of the values of Table 2 in the HCT reference match the contents of the hct column. Again I wonder if I'm missing something obvious :) Thanks for any insight! -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 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
Re: [gmx-users] Is it possible to run implicit solvent simulations in parallel?
Hi! If you are running implicit solvent with no cutoffs, ie using the special all-vs-all kernels, then particle decomposition will be used. This exact combination (gb, all-vs-all, dd) is quite tricky to implement, and is not supported at the moment, IIRC. This could be documented better, sorry. You could try changing constraints from all-bonds to h-bonds, meaning you will have only local constraints, which should allow you to run with particle decomposition. Or use a cut-off and domain decomposition. /Per 4 maj 2011 kl. 16.05 skrev Ozlem Ulucan: Dear Justin, this was only a test run and I ran the simulations on my multi-core workstations (4 cores actually). MPI is no longer required for such a situation. Since I did not set -nt option to 1, this can be accepted as a parallel run. So the command I sent in my previous e-mail was for the parallel run and for serial run I set -nt to 1. Dear Justin, as I said I am using a workstation of 4 processors. I have approximately 2200 atoms in my system. That means for one processor I have slightly more than 550 atoms. I set all the cut-offs to 0. I really need to run this system in parallel. Any suggestions to make it work out? Here is my run input file : ; ;File 'mdout.mdp' was generated ;By user: onbekend (0) ;On host: onbekend ;At date: Sun May 1 16:19:29 2011 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/roe include = ; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) define = ; RUN CONTROL PARAMETERS integrator = SD ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 50 ; For exact run continuation or redoing part of a run init_step= 0 ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 ; mode for center of mass motion removal comm-mode= Angular ; number of steps for center of mass motion removal nstcomm = 10 ; group(s) for center of mass motion removal comm-grps= system ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 10.0 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 1000 nstcalcenergy= -1 nstenergy= 1000 ; Output frequency and precision for .xtc file nstxtcout= 0 xtc-precision= 500 ; This selects the subset of atoms for the .xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = Protein ; Selection of energy groups energygrps = Protein ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 0 ; ns algorithm (simple or grid) ns_type = simple ; Periodic boundary conditions: xyz, no, xy pbc = no periodic_molecules = no ; nblist cut-off rlist= 0 ; long-range cut-off for switched potentials rlistlong= -1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = cut-off rcoulomb-switch = 0 rcoulomb = 0 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order
Re: [gmx-users] implicit solvent GB force table
Hi! The tabulated function is applied to all interactions, both bonded and non-bonded. The function is initialized in make_gb_table(), and accessed in the non-bonded kernels the same way as other tabulated functions are accessed. See GBtab[nnn] in the kernels for more details. In calc_gb_chainrule() the values of dadx (the derivative of the radii wrt. to the coordinates), and dvda (the derivative of the potential wrt. to the radii), which are calculated in the kernels, are simply multiplied together to yield the total force. Cheers /Per 31 mar 2011 kl. 21.09 skrev Chi-cheng Chiu: Hi, I have been tracking the code for implicit solvent, i.e. src/mdlib/genborn.c According to the gromacs paper on implicit solvent, J Comp Chem 31:2593, 2010, the GB force is tabulated in the X = Rij Ci Cj dimension. However, the tabulated function, which I think is stored in fr-gbtab, is only used in the function gb_bonds_tab(). I could not find the function of X applied in the calc_gb_chainrule() function. Does the gbtab applied on dvda and dadx elsewhere? Thanks in advance! regards, Chi-cheng -- 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
Re: [gmx-users] implicit solvent model: formulation of non-polar free energy
Hi! I know about this difference. The only reason for it is that, when I first started with this I used Tinker as a reference implementation, which has the 6-th power in the code. The differences should be small, though. The non-polar part only amounts to a few percent of the total force anyway. Cheers /Per 28 mar 2011 kl. 21:24 skrev Chi-cheng Chiu none0...@gmail.com: Hi everyone, I am going through the source code for the GB calculation part of gromacs, and found the following code in src/mdlib/genborn.c : in the function real calc_gb_nonpolar() rai = top-atomtypes.gb_radius[md-typeA[ai]]; rbi_inv = fr-invsqrta[ai]; rbi_inv2 = rbi_inv * rbi_inv; tmp = (rai*rbi_inv2)*(rai*rbi_inv2); tmp = tmp*tmp*tmp; e = factor*term*(rai+probe)*(rai+probe)*tmp; dvda[ai] = dvda[ai] - 6*e*rbi_inv2; es= es + e; so from this source code, energy seems to be (rai+probe)^2 * (rai/rbi)^6 where rbi is the born radius, rai is the atom radius, and probe is 0.14 nm. I checked the reference Schaefer et al. JMB 284(3):835–848, 1998 which is mentioned in the manual. It seems the reference used (rai+probe)^2 * (rai/rbi) where (rai/rbi) term don't have power of 6 and disagree with the source code. Is there a reason using power 6? Chi-cheng -- 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
Re: [gmx-users] IMPLICIT SOLVENT IN AMBER
Hi!
Starting an implicit solvent simulation works just as starting a normal,
explicit solvent simulation, except there is no solvent molecules.
You should use version 4.5.3 for this though (4.0.5 will not work).
Then you specify in the mdp-file implicit_solvent = GBSA and use pdb2gmx,
grompp, mdrun etc... as you otherwise would do.
The choice of the Born radii model is set by gb_algorithm = {Still,HCT,OBC} and
the non-polar solvation is calculated using sa_algorithm=Ace-approximation.
Cheers
/Per
10 mar 2011 kl. 10.10 skrev Yulian Gavrilov:
Dear, all
I just begin to work in gromacs.
I would like to run on a protein with amber99.
Is there someone here that successfully did a protein simulation in
GROMACS with implicit solvent and willing to explain the procedure and
share the parameters used (especially force field).
In mdout.mdp (gromacs 4.0.5) I found this lines. Can I add them to md.mdp?
How to change this parameters correctly?
What changes should be done on the previous steps? I mean, how to start a
simulation with implicit solvent model from the very beginning?
Sorry for primitive question, but I did not found any useful information
about it for the begginers.
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = No
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent = 80
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
sa_surface_tension = 2.092
--
Sincerely,
Yulian Gavrilov
--
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Re: [gmx-users] IMPLICIT SOLVENT IN AMBER
Hi!
The answer is that I do not now critical it is.
I have seen some papers that seem to hint at it not being overly critical, but,
again, life does not come at a net charge.
You'd have to see for yourself in your system, given the observables that are
important I suppose.
Possibly we can implement this in the future, as there indeed seems to be some
interest in it, but that is not a task I can deal with currently.
/Per
10 mar 2011 kl. 10.52 skrev Yulian Gavrilov:
Thanks again!
Don't you know how to make a total charge = 0 in this case, if implicit salt
concentration is not implemented currently? Or it is not critically?
2011/3/10 Per Larsson per.lars...@sbc.su.se
Hi!
Yes, except that in point 2, I'm not sure about the effects of explicit ions
in an implicit solvent.
Do deal with that properly one should use an implicit salt concentration, but
that is not implemented currently.
The choice of water-model with pdb2gmx is not important. You can choose
'None' here.
Cheers
/Per
10 mar 2011 kl. 10.39 skrev Yulian Gavrilov:
Thanks!
If I understand you correctly, I need to do this (?):
pdb2gmx
Adding ions (if I have no SOL, what is better to choose on this step?)
Minimization with mdp file, that includes these lines:
implicit_solvent = GBSA
gb_algorithm = {Still,HCT,OBC}
sa_algorithm=Ace-approximation
Equilibration (nvt, npt) and MD also with these lines in mdp files.
2011/3/10 Per Larsson per.lars...@sbc.su.se
Hi!
Starting an implicit solvent simulation works just as starting a normal,
explicit solvent simulation, except there is no solvent molecules.
You should use version 4.5.3 for this though (4.0.5 will not work).
Then you specify in the mdp-file implicit_solvent = GBSA and use pdb2gmx,
grompp, mdrun etc... as you otherwise would do.
The choice of the Born radii model is set by gb_algorithm = {Still,HCT,OBC}
and the non-polar solvation is calculated using
sa_algorithm=Ace-approximation.
Cheers
/Per
10 mar 2011 kl. 10.10 skrev Yulian Gavrilov:
Dear, all
I just begin to work in gromacs.
I would like to run on a protein with amber99.
Is there someone here that successfully did a protein simulation in
GROMACS with implicit solvent and willing to explain the procedure and
share the parameters used (especially force field).
In mdout.mdp (gromacs 4.0.5) I found this lines. Can I add them to md.mdp?
How to change this parameters correctly?
What changes should be done on the previous steps? I mean, how to start a
simulation with implicit solvent model from the very beginning?
Sorry for primitive question, but I did not found any useful information
about it for the begginers.
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = No
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent = 80
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
sa_surface_tension = 2.092
--
Sincerely,
Yulian Gavrilov
--
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--
Sincerely,
Yulian Gavrilov
--
Sincerely,
Yulian Gavrilov
--
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Re: [gmx-users] RE: g_energy inconsistent results
Hi! When you are computing your zero-step energies, do you then start from the gro-file that you got from em? If so, maybe the energies changes because gro-files have a fixed precision format (with three decimals), while the em-calculations are done using either full single or double precision. Your second issue is almost certainly related to rounding errors. The all-vs-all and the cutoff-code (even with enormous cut-offs) compute interactions in completely order. I would not worry about a 0.005 nm difference in RMSD. /Per 10 mar 2011 kl. 14.27 skrev Ehud Schreiber: Dear Mark Abraham (and anyone else interested), I have implemented your suggestion, changing in the status.mdp file to integrator = md and adding continuation = yes (this is the new name of the unconstrained_start parameter); however, this did not have any effect - the energy remained as before, different from the one obtained during the minimization. I have then encountered another (perhaps related) issue. I thought that the problem may arise from the combination of the generalized Born and all-vs-all settings. I have therefore changed in the minimization to rgbradii = rlist = rcoulomb = rvdw = 100 (from = 0). As my system is far smaller than 100 nm, I expected these parameters to provide also an all-vs-all setting (even if non-optimized). Nevertheless, the resulting structure differed from the previous minimized one (rmsd ~ 0.005 nm, delta energy ~ a few kJ/mol). Can this arise from rounding effects only or does this signify a problem? I'm not sure what rgbradii does, but the manual states that it must equal rlist. In addition, changing also status.mdp to have all radii = 100 and running on the new optimized output again does not yield the same energy as during the optimization. Does all of this make any sense to you? Thank, Ehud. Message: 6 Date: Tue, 08 Mar 2011 23:37:12 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] g_energy inconsistent results To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4d7622f8.7050...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 8/03/2011 9:44 PM, Ehud Schreiber wrote: Dear Gromacs users, I am working with version 4.5.3, using the opls-aa forcefield in an implicit solvent, all-vs-all setting: pdb2gmx -ter -ff oplsaa -water none -f file.pdb I am energy-minimizing structures in 3 stages (steep, cg and l-bfgs). The last stage is the following: grompp -f em3.mdp -p topol.top -c em2.gro -t em2.trr -o em3.tpr -po em3.mdout.mdp mdrun -nice 0 -v -pd -deffnm em3 g_energy -s em3.tpr -f em3.edr -o em3.potential_energy.xvg where the mdp file is: ;;; em3.mdp ;;; integrator = l-bfgs nsteps = 5 implicit_solvent = GBSA gb_algorithm = Still sa_algorithm = Ace-approximation pbc = no rgbradii = 0 ns_type = simple nstlist = 0 rlist= 0 coulombtype = cut-off rcoulomb = 0 vdwtype = cut-off rvdw = 0 nstcalcenergy= 1 nstenergy= 1000 emtol= 0 ;;; The last line in the em3.potential_energy.xvg file should give the (potential) energy of the minimized structure em3.gro . I wish also to compute the potential energy of .gro files in general, not necessarily obtained from a simulation. For that, I prepared a .mdp file for a degenerate energy minimization, having 0 steps, designed just to give the status of the file: Zero-step EM does not calculate the initial energy because it is not useful for gradient-based energy minimization. I don't recall the details, but perhaps the first EM step is reported as step zero. Instead, you should use zero-step MD (with unconstrained_start = yes), or (for multiple single points) mdrun -rerun. You will not necessarily reproduce the g_energy energies with anything, because the energy is dependent on the state of the neighbour lists. If nstenergy is a multiple of nstlist, then those energies should be fairly reproducible. I have updated the grompp source to provide a note to the user to warn against zero-step EM. Mark ;;; status.mdp ;;; integrator = l-bfgs nsteps = 0 implicit_solvent = GBSA gb_algorithm = Still sa_algorithm = Ace-approximation pbc = no rgbradii = 0 ns_type = simple nstlist = 0 rlist= 0 coulombtype = cut-off rcoulomb = 0 vdwtype = cut-off rvdw = 0 nstcalcenergy= 1 nstenergy= 1 emtol= 0 ;;; The only changes from the former .mdp file are in nsteps and nstenergy. However, when I run this potential
Re: [gmx-users] question about GBSA and opls-aa
Hi! The treatment of 1-2, 1-3 and 1-4 interactions with gbsa differ between the different born radii models, but not between force fields. For the Still model, polarisation energies are computed once for 1-2, 1-3 and 1-4 interactions, and never updated for these. For the HCT/OBC models, all interactions are included in the calculation of the born radii, and subsequently the polarisation energy, in every step. This is one of the reasons the Still model is faster, there are fewer calculations done per step. There is thus no special scaling for these interactions in any force field when computing the polarisation energy. They all contribute. For more details, please also read the original Still/HCT/OBC-papers. Regards /Per 28 feb 2011 kl. 16:51 skrev Baoqiang Cao bqcaom...@gmail.com: Hi, I'm using GBSA with opls-aa force field and have some questions that I couldn't find answers, I'd definitely be grateful if could get answer of tips. How does GBSA treat 1-2(covalent bonded), 1-3(bonded angle), 1-4(improper torsion) interactions? Should they all contribute nothing to GBSA energy or except 1-4? Thanks in advance! Baoqiang -- 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
Re: [gmx-users] Target implementation date for gb_saltconc?
Skickat från min iPhone 18 feb 2011 kl. 21:10 skrev Matthew Zwier mczw...@gmail.com: Dear GROMACS developers and users, Our research group is interested in performing GBSA simulations with GROMACS, but we would need to perform them with a nonzero salt concentration. I was wondering if there are plans to implement the gb_saltconc parameter, and if so, when it might become available. Many thanks, Matt Zwier University of Pittsburgh -- 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
Re: [gmx-users] OPLS implicit solvent problems
Hi! Thanks for pointing this out. It is unfortunate that they are missing from the gbsa.itp-file. I will add them, but I do not have time today. If you want to get going, you can add them yourself. The gb-parameters are essentially based on atom hybridization, so for each missing atom you find another that has the same (sp, sp2,sp3) hybridization, and add it to the gbsa.itp-file. Cheers /Per 21 jan 2011 kl. 13.51 skrev francesca.stanzi...@unina.it: Hello, I try to perform an implicit solvent simulation with Gromacs 4.5.3. version. I have a system corresponding to 6 peptides generated by Pymol with simmetrical cell, so I have a single PDB. I used OPLS-AA and i put the N-and C- termini as NH2 and COOH. My topology file is correct, and is all systems are included. ; Include forcefield parameters #include ./oplsaa.ff/forcefield.itp --- in this .itp file is included gbsa.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp #include topol_Protein_chain_C.itp #include topol_Protein_chain_D.itp #include topol_Protein_chain_E.itp #include topol_Protein_chain_F.itp ; Include water topology #include ./oplsaa.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include ./oplsaa.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 Protein_chain_C 1 Protein_chain_D 1 Protein_chain_E 1 Protein_chain_F 1 - When I start my simulations (md_start.mdp) in implicit solvent, i have this fatal error: GB parameter(s) missing or negative for atom type 'opls_912B' GB parameter(s) missing or negative for atom type 'opls_267' GB parameter(s) missing or negative for atom type 'opls_269' GB parameter(s) missing or negative for atom type 'opls_268' GB parameter(s) missing or negative for atom type 'opls_270' Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 1123 Fatal error: Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 5 atomtypes or they might be negative. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors. Controlling these atoms they corresponding to: opls_912B= the CA of N-terminal residue opls_267= Co in COOH opls_268= Oh in COOH opls_269= Oc in COOH neutral opls_270= H in COOH in the file gbsa.itp in opls.ff directory these atoms missing. Now, have I done something wrong? If is all ok, is it possible to create these missing atoms in the gbsa.itp file? thanx, francesca stanzione -- 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
Re: [gmx-users] van der Walls radius and implicit solvation
Hi! Currently there is no support in Gromacs for implicit solvation using a united-atom force field. It is definitely possible though, but you need to consult the literature for values for the radii. For united-atoms, I guess the hydrogens you mention are the polar hydrogens? All radii in the current implementation are taken from the literature, in many cases though using Tinker as the primary source. Cheers /Per 11 jan 2011 kl. 19.19 skrev Diogo Vila Viçosa: Hi, I have two questions regarding the generalized born models implemented in GROMACS. 1) Is it possible to perform an MD run using implicit solvent with an united-atom force field? If so, how are determined the van der Walls radii for H atoms? 2) How are determined the other van der walls radii used in GROMACS? Thanks in advance Diogo Vila Viçosa -- 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
Re: [gmx-users] Re: gb_saltconc in implicit water simulations
Hi! Which results can you not recreate? Yes - all simulations were run at zero salt concentration. Implicitly this means that we did not do anything special to treat the charges. The protein has an overall charge of -2, looking at the topology. In hindsight, we probably should have given this issue more thought, but for assessing the correctness of the CHARMM implementation (the parameters) it seemed not so important, I'm afraid. For the sa_algorithm option, this seems weird. If I try to set sa_algorithm = Still, I get an error as it is not yet implemented. The only viable options are etiher None or Ace-approximation. If you want to mail me your input-files off-list, I will have a look after Christmas. Cheers /Per 22 dec 2010 kl. 03.23 skrev Rogan Carr: Hi Per (and all), I am trying to recreate the results of the CHARMM forcefield implementation to better understand how to implement implicit solvent models, but I can't quite recreate your results. If the Gromacs code doesn't use salt concentrations, does that mean that your simulations were run at zero salt concentration? Also, how did you deal with the charged residues on the protein? Also, sort of on the same topic, no matter what option I choose for sa_algorithm with Gromacs 4.5.3, it always uses sa_algorithm=Still. Thanks for your help, Rogan On Dec 14, 2010, at 12:13 PM, Per Larsson wrote: Hi! Sorry that I missed this discussion, we recently moved the lab and there where quite many things to attend to. When we did the implementation of implicit solvent into Gromacs, one of the strong points was to see how fast we could make it, to speed up conformational sampling as much as possible. Adding in the extra Debye-Huckel term for a non-zero salt-concentration was not a priority at the time. It might be a bit unfortunate that the option anyway exists in the mdp-file. I will try and see if I can find the time to put it in, but that will not happen in the next coming weeks although I agree that it would be very useful to have :-) When it comes to the use of explicit ions in an implicit solvent, I hate to say that I'm not much of an expert, really. Having said that, and someone else is very welcome to correct me on this point, there does not seem to exist a wide body of literature about this. In addition to the paper that Justin pointed to, there is some work done by Michael Feig (eg. http://www.ncbi.nlm.nih.gov/pubmed/16928023). Also I think that particularly with DNA there are problems with the theory itself as it does not handle high salt-concentrations very well. Cheers /Per 14 dec 2010 kl. 20.22 skrev devicerandom: On 14/12/10 19:04, Justin A. Lemkul wrote: I was going to send a very similar mail -namely, I have a coarse-grain system in vacuum where I'd like to simulate a charged polymer. My idea was that of adding a single ghost counter-ion with zero VdW interactions, perhaps keeping it fixed in one corner of the box, but I'd like to know how meaningful it is. In vacuum and implicit solvent are very different concepts. If you are indeed simulating in a vacuum, I would be willing to bet that your charged polymer will rapidly associate with your dummy ion simply due to attractive Coulombic interactions that are not screened by any intervening solvent. Heh, I know very well that -and that is one of the reasons I wanted to know how does one cope with that. I mean, if it's a single polymer, perhaps one can naively position restrain the ion in a corner of the box, away from the polymer, while the polymer stays on its center of mass. But if I want multiple objects in my box, I guess it's not going to work. I'd like very much to use implicit solvent as well but I have to see how deep is the performance impact on my model -after all, one does coarse grain to be raw but *fast* :) In regards to the original post, I have seen this question asked and ignored several times already, unfortunately. Most of the literature I have read (which primarily uses CHARMM) does not specify how counterions are handled, if at all. Maybe there is some intrinsic compensating factor in CHARMM that I simply don't know about. I found this: http://dx.doi.org/10.1002/jcc.20874 But again, it uses CHARMM and fancy modified electrostatic models. I would really hope that someone who knows about the proper GROMACS methodology would comment. This has been a curiosity of mine for some time, as well. I have not had a pressing need to try out the implicit solvent features, but in the absence of being sure of the methodology, I am unlikely to do so. Perhaps the developers of the implicit solvent know about that? I hope so... m. -- 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
Re: [gmx-users] Re: gb_saltconc in implicit water simulations
Hi! Sorry that I missed this discussion, we recently moved the lab and there where quite many things to attend to. When we did the implementation of implicit solvent into Gromacs, one of the strong points was to see how fast we could make it, to speed up conformational sampling as much as possible. Adding in the extra Debye-Huckel term for a non-zero salt-concentration was not a priority at the time. It might be a bit unfortunate that the option anyway exists in the mdp-file. I will try and see if I can find the time to put it in, but that will not happen in the next coming weeks although I agree that it would be very useful to have :-) When it comes to the use of explicit ions in an implicit solvent, I hate to say that I'm not much of an expert, really. Having said that, and someone else is very welcome to correct me on this point, there does not seem to exist a wide body of literature about this. In addition to the paper that Justin pointed to, there is some work done by Michael Feig (eg. http://www.ncbi.nlm.nih.gov/pubmed/16928023). Also I think that particularly with DNA there are problems with the theory itself as it does not handle high salt-concentrations very well. Cheers /Per 14 dec 2010 kl. 20.22 skrev devicerandom: On 14/12/10 19:04, Justin A. Lemkul wrote: I was going to send a very similar mail -namely, I have a coarse-grain system in vacuum where I'd like to simulate a charged polymer. My idea was that of adding a single ghost counter-ion with zero VdW interactions, perhaps keeping it fixed in one corner of the box, but I'd like to know how meaningful it is. In vacuum and implicit solvent are very different concepts. If you are indeed simulating in a vacuum, I would be willing to bet that your charged polymer will rapidly associate with your dummy ion simply due to attractive Coulombic interactions that are not screened by any intervening solvent. Heh, I know very well that -and that is one of the reasons I wanted to know how does one cope with that. I mean, if it's a single polymer, perhaps one can naively position restrain the ion in a corner of the box, away from the polymer, while the polymer stays on its center of mass. But if I want multiple objects in my box, I guess it's not going to work. I'd like very much to use implicit solvent as well but I have to see how deep is the performance impact on my model -after all, one does coarse grain to be raw but *fast* :) In regards to the original post, I have seen this question asked and ignored several times already, unfortunately. Most of the literature I have read (which primarily uses CHARMM) does not specify how counterions are handled, if at all. Maybe there is some intrinsic compensating factor in CHARMM that I simply don't know about. I found this: http://dx.doi.org/10.1002/jcc.20874 But again, it uses CHARMM and fancy modified electrostatic models. I would really hope that someone who knows about the proper GROMACS methodology would comment. This has been a curiosity of mine for some time, as well. I have not had a pressing need to try out the implicit solvent features, but in the absence of being sure of the methodology, I am unlikely to do so. Perhaps the developers of the implicit solvent know about that? I hope so... m. -- 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
Re: [gmx-users] Thermostat for REMD simulations in implicit solvent
Hi! Have never tried remd with implicit solvent, but note that the unit of tau-t in the mdp-file is ps, not ps-1. This means you should set tau-t = 0.0109 rather than 91. Try this and see if the problem goes away! /Per 26 nov 2010 kl. 15:55 skrev César Ávila clav...@gmail.com: Dear all, I am trying to set up a REMD simulation for a peptide (CHARMM ff) in implicit solvent (OBC GB). Following Bjelkmar et al* I am using stochastics dynamics integration with an inverse friction constant of 91 ps-1, 5 fs timestep, virtual-sites for hydrogens, all-vs-all nonbonded (no cutoff). The full .mdp file is attached at the end of this mail. The problem I am facing is that after a while, the temperatures of all replicas start dropping even below the lowest target temperature. Would you suggest changing some parameter or the whole thermostat to prevent this from happening? @ s0 legend Temperature 0.00 310.811523 5.00 435.627045 10.00 417.161713 15.00 414.248901 20.00 399.390686 25.00 375.087219 30.00 338.131256 35.00 339.961151 40.00 319.424561 45.00 290.442322 50.00 289.587921 55.00 248.746246 60.00 253.192047 65.00 242.619476 70.00 256.051941 75.00 237.648468 80.00 231.938690 85.00 217.029953 90.00 211.447983 95.00 210.393890 100.00 208.518417 105.00 196.718445 110.00 219.245682 115.00 202.957993 120.00 193.128159 125.00 198.278198 130.00 175.304108 135.00 164.925613 140.00 195.024490 145.00 201.153046 150.00 211.160797 155.00 189.525085 160.00 191.156006 165.00 186.545242 170.00 186.885422 175.00 182.838486 180.00 174.960098 185.00 175.244049 190.00 179.517975 195.00 165.785416 200.00 189.871048 205.00 179.510178 210.00 152.527710 215.00 160.109955 220.00 163.564148 * Implementation of the CHARMM ff in GROMACS (2010) JCTC, 6, 459-466 ; Run parameters integrator = sd dt = 0.005; ps ! nsteps = 2 nstcomm = 1 comm_mode = angular ; non-periodic system ; Bond parameters constraints = all-bonds constraint_algorithm= lincs lincs-iter = 1 lincs-order = 6 ; required cutoffs for implicit nstlist = 0 ns_type = grid rlist = 0 rcoulomb= 0 rvdw= 0 epsilon_rf = 0 rgbradii= 0 ; cutoffs required for qq and vdw coulombtype = cut-off vdwtype = cut-off ; temperature coupling tcoupl = v-rescale tc-grps = system tau-t = 91 ref-t = 300 ; Pressure coupling is off Pcoupl = no ; Periodic boundary conditions are off for implicit pbc = no ; Settings for implicit solvent implicit_solvent= GBSA gb_algorithm= OBC gb_epsilon_solvent = 78.3 sa_surface_tension = 2.25936 ;Output control nstxout = 1000 nstfout = 0 nstvout = 0 nstxtcout = 0 nstlog = 1000 nstcalcenergy = -1 nstenergy = 1000 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 300 gen_seed = 1993 -- 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
Re: [gmx-users] Using Charmm FF with implicit solvent on gromacs
Hi! Currently it is not possible to use GBSW in Gromacs. As you noted, there are three GB-models available (Still,HCT,OBC), that can be run using plain cutoffs (or no cutoffs at all, using the optimized all-vs-all kernels). Currently there is unfortunately no work being done to extend the range of implicit solvent models available. However, we have had some promising results with the combination of CHARMM FF + CMAP + OBC, as discussed in the 2010 JCTC paper. Cheers /Per 18 nov 2010 kl. 22.49 skrev César Ávila: Dear all, I would like to know if anyone has experience on running simulations using the Charmm FF and implicit solvent model on gromacs. I have found that gromacs has three implementations for GB models Still Hawkins-Cramer-Truhlar (HCT) Onufriev-Bashford-Case (OBC) The charmm FF has been extensively tested with the GBSW* implementation (in Charmm program) for which the backbone phi/psi cross-term (CMAP) and the atomic input radii were specifically optimized (Chan, Im and Brooks, JACS, 2006). Is there a way to perform the same calculation on gromacs? * W. Im, M.S. Lee, and C.L. Brooks III Generalized Born Model with a Simple Smoothing Function. J. Comput. Chem. 24:1691-1702 (2003). -- 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
Re: [gmx-users] Role of epsilon_rf in implicit solvation
Hi! It would be nice to have reaction-field for GB as well, but currently this is not the case. The polarisation energy is scaled using (1.0/epsilon_r - 1.0/gb_epsilon_solvent) always, epsilon_rf is never used. Cheers /Per 19 nov 2010 kl. 12.30 skrev Christian Mücksch: So is this epsilon_rf also used in combination in implicit solvent models regarding the dielectric constant beyond cut-off? If yes, what would be an appropriate value for this constant? -- 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] Re: GB-polarization
Hi! Sorry for the confusion here. Justin is right. In versions before 4.5.2, the non-polar solvation calculation was done regardless of the sa_algorithm setting. In 4.5.2, this has to be specified explicitly using the setting Ace-approximation, to get the complete solvation free energy. Also, the value of sa_surface_tension was set automatically in versions up to 4.5.1. In 4.5.2, this is also the case as long as it is set to -1 in the mdp-file. Setting it to 0 means no non-polar calculation is done, and setting it to something else (but non-zero) will override the default values (eg. those that were always used in 4.5.1) Again, sorry for the confusion. I will update the manual to make this more clear. /Per Skickat från min iPhone 9 nov 2010 kl. 23:53 skrev Justin A. Lemkul jalem...@vt.edu: Christian Mücksch wrote: But in order to get the complete solvation free energy these calculations for the van der Waals and cavity terms have to be done. So does that mean that the solvation free energy calculated by default without specifying sa_algorithm=Ace-approximation is missing these terms? I thought that the ACE-type approximation is done by default (due to the manual) when using GBSA. I think it all depends on the version you're using. Ace-approximation became default in version 4.5.2 (I think). In previous versions, no was the default, at least such was the case in my testing of 4.5.1. -Justin Kind regards, Christian Christian Mücksch wrote: Thanks for the clarification but I can't find anything in the .log or .edr-files that would correspond to the non-polar solvation energy. I think you have to set sa_algorithm=Ace-approximation for this calculation to be done, and thus written. -Justin Christian Mücksch Department of Physics TU Kaiserslautern Erwin Schrödinger Straße 67663 Kaiserslautern Germany Phone: +49 (0)631 205 4287 Fax: +49 (0)631 205 4965 Email:mueck...@rhrk.uni-kl.de Hi! Yes, the GB-polarization energy corresponds to the solvent-solute electrostatics polarization energy. The non-polar part of the solvation energy (the solvent-solvent cavity term and the solute-solvent vdw-term) are named Non. polar solvation (or something like that) in the log-file. /Per 4 nov 2010 kl. 11.10 skrev Christian Mücksch: Dear all, I've got a general question regarding implicit solvent simulations. Using g_energy there's an option to print out the GB-polarization. Is that the solvent-solute electrostatics polarization free energy? How can one interpret a rise or decrease in the GB-polarization? Kind regards, -- 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 -- 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 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] GB-polarization
Hi! Yes, the GB-polarization energy corresponds to the solvent-solute electrostatics polarization energy. The non-polar part of the solvation energy (the solvent-solvent cavity term and the solute-solvent vdw-term) are named Non. polar solvation (or something like that) in the log-file. /Per 4 nov 2010 kl. 11.10 skrev Christian Mücksch: Dear all, I've got a general question regarding implicit solvent simulations. Using g_energy there's an option to print out the GB-polarization. Is that the solvent-solute electrostatics polarization free energy? How can one interpret a rise or decrease in the GB-polarization? Kind regards, -- Christian Mücksch Department of Physics TU Kaiserslautern Erwin Schrödinger Straße 67663 Kaiserslautern Germany Phone: +49 (0)631 205 4287 Email: mueck...@rhrk.uni-kl.de -- 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
Re: [gmx-users] about sa_surface_tension
Hi! This is unfortunately a bit confusing, but prior to the release of 4.5.2 gromacs did not use the value of the sa_surface_tension that was specified in the mdp-file. It was always set to 2.092, and then hardcode to take a certain value (other than 2.092) depending on the GB-model. 2.25936 is the value used together with OBC/HCT models, it is slightly lower with the Still model. In 4.5.2 the default will be -1, which, if left unchanged, will be changed to proper values (and a note written about this). The effect on the result will be very small, since the sa_surface_tension-parameter is only used for the non-polar part of solvation, which in turn is a very minor part of the total force. Also in 4.5.2, setting sa_surface_tension=0 means that no non-polar solvation is being calculated. Sorry for the confusion /Per 18 okt 2010 kl. 14.07 skrev Christian Mücksch: Dear all, when using implicit solvent models, the sa_surface_tension parameter is set to 2.092 kJ/mol/nm2 by default. However in Gromacs benchmarks with dihydrofolate reductase this parameter is set to 2.25936. Can someone please explain this parameter and in how far this would change the simulation outcome. Kind regards, -- Christian Mücksch Department of Physics TU Kaiserslautern Erwin Schrödinger Straße 67663 Kaiserslautern Germany Phone: +49 (0)631 205 4287 Email: mueck...@rhrk.uni-kl.de -- 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
Re: [gmx-users] best parameters for energy determination with GBSA
Hi Ehud! Your settings are correct. However, you can also use domain decomposition with GB, and I at least usually bypass the editconf stage, and do pdb2gmx-grompp-mdrun, when you do not want any pbc. /Per 7 okt 2010 kl. 12.29 skrev Ehud Schreiber: Dear GROMACS users, I try to compute energies of a small peptide-domain complex and of its constituents using implicit solvent, so that I can get the binding Delta E. I need the accuracy to be high enough so that I can reliably measure the Delta Delta E between the wildtype peptide and a mutation of it. I would like to get advice as to the best setting and parameters to use; are the ones given below the correct and best ones (most in an mdp file, some run control parameters of GROMACS commands)? Are other defaults in need to be changed? As the GBSA method necessitates using the inexact cut-off interactions, and my system is rather small, I consider using no cut-off at all, i.e. an all-vs.-all approach. For that I understand the parameters should be nstlist=0 ns_type=simple -pd ; in mdrun coulombtype=cut-off rcoulomb=0 vdwtype=cut-off rvdw=0 rlist=0 Then, there are the implicit solvent parameters themselves: implicit_solvent=GBSA gb_algorithm= Still sa_algorithm=Ace-approximation rgbradii=0 Finally, regarding the simulation box, I see no need for periodic boundary conditions, and I pick some big margin around the system (as there are no water molecules, no need to spare): pbc=no -d 5.0 ; in editconf What do you say? Thanks, Ehud. -- 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
Re: [gmx-users] potential energy in implicit solvent simulations
Hi It seems that the non-polar energy term has gone missing, and does not get included in the print-out. While adding it back again properly I found some other issues that I need to check before committing. The total potential energy should be correct. /Per 16 sep 2010 kl. 17:47 skrev Ehud Schreiber schr...@compugen.co.il: Can you explain this situation? -- 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] About implicit water simulations
Hi! This is not something that is planned for the immediate future, as useful as it might be. However, for small to medium sized systems one can get good performance by using the all-vs-all kernels. Then the problem of poor energy conservation disappears. Cheers /Per Skickat från min iPhone 9 sep 2010 kl. 15:54 skrev Christian Mücksch mueck...@rhrk.uni-kl.de: Dear users, I got a question concerning simulations with implicit solvent. So far it is only possible to use this model when applying a cut-off for the long range electrostatic and vdW interactions which leads to bad energy conservation etc. Will there be an update allowing to use reaction-field for instance or user-defined potentials with implicit solvent models? Best regards, Christian Mücksch -- Christian Mücksch Phone: +49 (0)631 205 4287 Department of Physics Fax: +49 (0)631 205 4965 TU Kaiserslautern Email: mueck...@rhrk.uni-kl.de Erwin Schrödinger Straße 67663 Kaiserslautern Germany -- 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
Re: [gmx-users] Generalized Born segfaults with v4.5.1
Hi! I am currently working on another issue with the GB-double precision loops. I'll include this as well. But your pdb-file only contains 1 residue with the name UNK (by openBabel). Could you please send me another pdb-file that reproduces this error off-list, and I'll get to it. Cheers /Per 7 sep 2010 kl. 09.59 skrev Silvio a Beccara: Dear friends, when trying to run a double precision vanilla MD, version 4.5.1, with a small hairpin molecule (248 atoms) in implicit solvent (generalized Born approximation) this is what I get: - Getting Loaded... Reading file hairpin-md-gb-1.tpr, VERSION 4.5.1 (double precision) Loaded with Money starting mdrun 'Protein' 5 steps, 50.0 ps. Segmentation fault - In some trials, I also get a message about the distance in an 1-4 interaction being beyond the table size, but this is not the case. Strangely enough, the MD runs fine with a development version (4.0.99, downloaded from the GIT repository). I am attaching my mdp and pdb files. Regards Silvio a Beccara Dip. di Fisica - Universita` di Trento 14 Via Sommarive 38123 Povo - TN tel: 0461-881631 md-gb.mdpratch-frame63.pdb-- 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
Re: [gmx-users] grompp_d and mdrun_d issues with GBSA and normal mode analysis
This has been fixed with Berk's commit c06ee471... The error was not related to GB, but rather a combination of domain decomp.+nm+cut-offs. Cheers /Per 6 sep 2010 kl. 11.38 skrev Ehud Schreiber: Dear GROMACS users, I am encountering a couple of issues when trying to perform normal mode analysis in an implicit solvent (GBSA) setting. I am using version 4.5.1 with double precision; unfortunately I do not have the single precision version installed for comparison. The starting point is a small protein which was energy minimized in two stages, also in double precision and with GBSA, producing “em2” files. The mdp file used for the normal mode analysis is the following: - nm.mdp - integrator = nm nsteps = 1 implicit_solvent = GBSA gb_algorithm = Still ; the default rgbradii = 1.0 ; must be equal to rlist rlist= 1.0 coulombtype = cut-off rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 --- The command used is grompp_d -f nm.mdp -p topol.top -c em2.gro -t em2.trr -o nm.tpr which ran fine except for the following note: NOTE 1 [file nm.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Then, I tried to run mdrun_d -v -nice 0 -deffnm nm However, the command seems to be stuck, and the following serious warning is produced: Warning: 1-4 interaction between 64 and 71 at distance 3.114 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Maximum force: 3.48709e+06 Maximum force probably not small enough to ensure that you are in an energy well. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. The em2.gro is definitely not having such a large distance between atoms 64 and 71: 6GLN CB 64 1.879 1.895 2.423 . . 6GLNOE1 71 2.047 1.715 2.642 which are only about 0.346 nm apart. Also, the energy minimization, which used the same options, mutatis mutandis, -- em2.mdp -- integrator = cg nsteps = 1000 nstcgsteep = 40 implicit_solvent = GBSA gb_algorithm = Still ; the default rgbradii = 1.0 ; must be equal to rlist nstlist = 10 rlist= 1.0 coulombtype = cut-off rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 nstenergy= 10 - converged to machine precision having a much smaller maximum force: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Polak-Ribiere Conjugate Gradients converged to machine precision in 0 steps, but did not reach the requested Fmax 10. Potential Energy = -2.71868395521758e+04 Maximum force = 4.63436548427712e+02 on atom 584 Norm of force = 1.25296847735530e+02 The other problem arises when I try to follow the grompp_d note above and change in nm.mdp to coulombtype = pme I then have a fatal error: ERROR 1 [file nm.mdp]: With GBSA, coulombtype must be equal to Cut-off Am I doing something wrong or are there still some problems in the new GBSA option of version 4.5.1? Thanks, Ehud Schreiber. -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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] grompp_d and mdrun_d issues with GBSA and normal mode analysis
Hi! This should work. I checked the code but did not find anything obvious. Could you please file a bugzilla and I'll have a look as soon as possible. Thanks! /Per 6 sep 2010 kl. 11.38 skrev Ehud Schreiber: Dear GROMACS users, I am encountering a couple of issues when trying to perform normal mode analysis in an implicit solvent (GBSA) setting. I am using version 4.5.1 with double precision; unfortunately I do not have the single precision version installed for comparison. The starting point is a small protein which was energy minimized in two stages, also in double precision and with GBSA, producing “em2” files. The mdp file used for the normal mode analysis is the following: - nm.mdp - integrator = nm nsteps = 1 implicit_solvent = GBSA gb_algorithm = Still ; the default rgbradii = 1.0 ; must be equal to rlist rlist= 1.0 coulombtype = cut-off rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 --- The command used is grompp_d -f nm.mdp -p topol.top -c em2.gro -t em2.trr -o nm.tpr which ran fine except for the following note: NOTE 1 [file nm.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Then, I tried to run mdrun_d -v -nice 0 -deffnm nm However, the command seems to be stuck, and the following serious warning is produced: Warning: 1-4 interaction between 64 and 71 at distance 3.114 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Maximum force: 3.48709e+06 Maximum force probably not small enough to ensure that you are in an energy well. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. The em2.gro is definitely not having such a large distance between atoms 64 and 71: 6GLN CB 64 1.879 1.895 2.423 . . 6GLNOE1 71 2.047 1.715 2.642 which are only about 0.346 nm apart. Also, the energy minimization, which used the same options, mutatis mutandis, -- em2.mdp -- integrator = cg nsteps = 1000 nstcgsteep = 40 implicit_solvent = GBSA gb_algorithm = Still ; the default rgbradii = 1.0 ; must be equal to rlist nstlist = 10 rlist= 1.0 coulombtype = cut-off rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 nstenergy= 10 - converged to machine precision having a much smaller maximum force: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Polak-Ribiere Conjugate Gradients converged to machine precision in 0 steps, but did not reach the requested Fmax 10. Potential Energy = -2.71868395521758e+04 Maximum force = 4.63436548427712e+02 on atom 584 Norm of force = 1.25296847735530e+02 The other problem arises when I try to follow the grompp_d note above and change in nm.mdp to coulombtype = pme I then have a fatal error: ERROR 1 [file nm.mdp]: With GBSA, coulombtype must be equal to Cut-off Am I doing something wrong or are there still some problems in the new GBSA option of version 4.5.1? Thanks, Ehud Schreiber. -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ffamber03 H0 atomtype in 4.5.1
Hi! This seems to be an unfortunate mistake. It should not be commented out. Thank you for reporting this, I will fix it for the next release. Cheers /Per 6 sep 2010 kl. 17.08 skrev William Joseph Allen: Hello Gromacs users, I have recently set up some simulations of a peptide using the amber03 force field in 4.5.1 and implicit solvent. When I run it through grompp, it gives me the following: --- Program grompp-4.5.1, VERSION 4.5.1 Source code file: grompp.c, line: 870 Fatal error: Can't do GB electrostatics; the forcefield is missing 1 values for atomtype radii, or they might be negative . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The missing value it is referring to was also mentioned in the grompp output: *** GB parameter(s) missing or negative for atom type 'H0' *** The 'H0' (read h-zero) atomtype only appears in glycine residues. It is equivalent in all ways to the 'H1' (read h-one) atomtype. But for some reason, in the gbsa.itp file, the 'H0' atomtype is commented out. When it is un-commented, grompp proceeds as normal. My question is why is this specific atomtype commented out in the amber03 gbsa.itp file? Thanks in advance, Joe -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GB Parameters
Hi! You are correct, expect that the values in column 4 (the Vdw-radii for atom types) that are being used to calculate the Born radii currently are force field and radii-algorithm agnostic (as is indeed the case in Tinker as well). Obviously, if someone wants to use other Vdw-radii, such as eg. the Bondi, these values will need to be changed. Good luck! /Per 24 aug 2010 kl. 13.05 skrev Elizabeth Ploetz: Greetings! Thank you both for such timely and helpful responses. Below I have listed how I (and anyone interested in using their own force field) should modify the gbsa.itp file, according to my new understanding. Please let me know if I am wrong. Columns 1-3: Leave them alone, they are not used in 4.5beta3 Column 4: Use the force field's LJ sigma/2 (except for hydrogen: use 0.115 regardless of the hydrogen's sigma value) Column 5: Leave it as is, because the HCT scaling factors are not force field specific Prof. van der Spoel, unfortunately our force field does not support nucleic acids either. Per, I will let you know if I find any errors, however I am new to implicit solvent methods, so I have a lot of learning to do first! Best, E. A. Ploetz - Original Message - From: gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent: Tuesday, August 24, 2010 2:51:14 AM Subject: gmx-users Digest, Vol 76, Issue 120 Send gmx-users mailing list submissions to gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: GB Parameters (Per Larsson) 2. Re: Charmm to Gromacs: Polyols force field [Justin] (Bruce D. Ray) 3. Re: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Mark, Justin] (Eudes Fileti) 4. Re: Does anyone know how to get the file charmm_gromacs.tar.gz? (Mark Abraham) 5. gmx 4.5 and openmm on Mac, still not compiling (Alan) -- Message: 1 Date: Mon, 23 Aug 2010 20:41:51 +0200 From: Per Larsson per.lars...@sbc.su.se Subject: Re: [gmx-users] GB Parameters To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 21e19e54-404f-42d2-8ddc-0684c6bb9...@sbc.su.se Content-Type: text/plain; charset=us-ascii Also, again, as David said, if you find any errors in the parameters or in the code, please let me know! Cheers /Per 23 aug 2010 kl. 20:09 skrev Per Larsson per.lars...@sbc.su.se: Hi! Values in columns 1-3 are not currently used in version beta3. They pertain to more elaborate surface area algorithms, the one from Still et al in particular. Column 4 is the Vdw-radii for atom types that are used for computing the Born radii. The dielectric offset is specified in the mdp-file, and gets added to the input radii for the different radii methods. Column 5 is the scale factor for the HCT/OBC models. The values are taken from the original HCT reference, as well as the corresponding implementation in Tinker. /Per 23 aug 2010 kl. 19:27 skrev Elizabeth Ploetz plo...@ksu.edu: Dear Gromacs Users, I am interested in implementing implicit solvent using the OBC GBSA method. In the Gromacs 4.5beta3 top directory, several force fields (oplsaa and multiple versions of amber) contain the gbsa.itp file, and one (charmm27), contains a gb.itp file. They all have the same column titles (sar, st, pi, gbr, and hct). I have read the six articles listed at http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent, however I still have the following two questions regarding the contents of this file: (1.) What values are tabulated in these columns and what are the corresponding references for each of them? (2.) Which columns are used (versus ignored) by Gromacs in the implementation of each of the methods (Still/HCT/OBC)? Here are my guesses for Question 1: (a.) sar: solvent accessible surface area? (b.) st: surface tension? (c.) pi: ? (d.) gbr: generalized born radius? These values correspond to sigma/2 from Jorgensen and Tirado-Rives' 1988 JACS paper (v. 110, p. 1657). However the generalized born radius is equal to Rvdw plus a dielectric offset distance, according to Still et al's 1997 J. Phys. Chem. A paper (v. 101, p. 3005). This would mean the dielectric offset distance is set to zero (?). (e.) hct: HCT parameter With an eventual goal of implementing implicit solvent using my lab's force field, insight into the meaning of the columns and/or references for their origin would be greatly
Re: [gmx-users] GB Parameters
Hi! Values in columns 1-3 are not currently used in version beta3. They pertain to more elaborate surface area algorithms, the one from Still et al in particular. Column 4 is the Vdw-radii for atom types that are used for computing the Born radii. The dielectric offset is specified in the mdp-file, and gets added to the input radii for the different radii methods. Column 5 is the scale factor for the HCT/OBC models. The values are taken from the original HCT reference, as well as the corresponding implementation in Tinker. /Per 23 aug 2010 kl. 19:27 skrev Elizabeth Ploetz plo...@ksu.edu: Dear Gromacs Users, I am interested in implementing implicit solvent using the OBC GBSA method. In the Gromacs 4.5beta3 top directory, several force fields (oplsaa and multiple versions of amber) contain the gbsa.itp file, and one (charmm27), contains a gb.itp file. They all have the same column titles (sar, st, pi, gbr, and hct). I have read the six articles listed at http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent, however I still have the following two questions regarding the contents of this file: (1.) What values are tabulated in these columns and what are the corresponding references for each of them? (2.) Which columns are used (versus ignored) by Gromacs in the implementation of each of the methods (Still/HCT/OBC)? Here are my guesses for Question 1: (a.) sar: solvent accessible surface area? (b.) st: surface tension? (c.) pi: ? (d.) gbr: generalized born radius? These values correspond to sigma/2 from Jorgensen and Tirado-Rives' 1988 JACS paper (v. 110, p. 1657). However the generalized born radius is equal to Rvdw plus a dielectric offset distance, according to Still et al's 1997 J. Phys. Chem. A paper (v. 101, p. 3005). This would mean the dielectric offset distance is set to zero (?). (e.) hct: HCT parameter With an eventual goal of implementing implicit solvent using my lab's force field, insight into the meaning of the columns and/or references for their origin would be greatly appreciated. Thanks in advance! Sincerely yours, E. A. Ploetz -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GB Parameters
Also, again, as David said, if you find any errors in the parameters or in the code, please let me know! Cheers /Per 23 aug 2010 kl. 20:09 skrev Per Larsson per.lars...@sbc.su.se: Hi! Values in columns 1-3 are not currently used in version beta3. They pertain to more elaborate surface area algorithms, the one from Still et al in particular. Column 4 is the Vdw-radii for atom types that are used for computing the Born radii. The dielectric offset is specified in the mdp-file, and gets added to the input radii for the different radii methods. Column 5 is the scale factor for the HCT/OBC models. The values are taken from the original HCT reference, as well as the corresponding implementation in Tinker. /Per 23 aug 2010 kl. 19:27 skrev Elizabeth Ploetz plo...@ksu.edu: Dear Gromacs Users, I am interested in implementing implicit solvent using the OBC GBSA method. In the Gromacs 4.5beta3 top directory, several force fields (oplsaa and multiple versions of amber) contain the gbsa.itp file, and one (charmm27), contains a gb.itp file. They all have the same column titles (sar, st, pi, gbr, and hct). I have read the six articles listed at http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent, however I still have the following two questions regarding the contents of this file: (1.) What values are tabulated in these columns and what are the corresponding references for each of them? (2.) Which columns are used (versus ignored) by Gromacs in the implementation of each of the methods (Still/HCT/OBC)? Here are my guesses for Question 1: (a.) sar: solvent accessible surface area? (b.) st: surface tension? (c.) pi: ? (d.) gbr: generalized born radius? These values correspond to sigma/2 from Jorgensen and Tirado-Rives' 1988 JACS paper (v. 110, p. 1657). However the generalized born radius is equal to Rvdw plus a dielectric offset distance, according to Still et al's 1997 J. Phys. Chem. A paper (v. 101, p. 3005). This would mean the dielectric offset distance is set to zero (?). (e.) hct: HCT parameter With an eventual goal of implementing implicit solvent using my lab's force field, insight into the meaning of the columns and/or references for their origin would be greatly appreciated. Thanks in advance! Sincerely yours, E. A. Ploetz -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] cutoff for implicit solvent in gromacs4.5
Hi, for implicit solvent, people generally use longer cut-offs, as you noted. There can be many reasons for your seg. fault, however. Did you do energy minimization before starting md? Please also test the same system with using a cut-off to see if that works. /Per 8 aug 2010 kl. 22.36 skrev BIN ZHANG: But the problem is with this set up, I will always get a Segmentation fault with gromacs VERSION 4.5-beta2. Is this supposed to be a bug or for this version, I can only use a large cutoff? -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] new beta release - gromacs-4.5-beta2
Hi! Is this with GBSA implicit solvent, and in that case what Born radii model? Could you mail me the tpr off-list, and I'll have a look at it. Cheers /Per 5 aug 2010 kl. 20.26 skrev Elio Cino: Since the charmm force field has some instances with large charge groups (grompp warns you for it) it is advisable to use a longer cut-off (or no cut-off at all, by setting them all to 0). I've run 200 ns simulations with 1.5 nm and nstlist = 5 and a timestep of 2 fs and constraints = all-bonds. I could not have them set to infinite because I am using PBC. I used 1.5 and the system ran fine with 2fs timestep. On another note, I installed 4.5 beta2 on another computer today and using the exact same system and settings I get tons of lincs errors (bond rotate over 30 deg) and cannot even do position restrain dynamics without segmentation fault. I even tried using the exact same tpr files as my successful runs. The one that works was my laptop (OSX 10.6 core2 duo) and the one that fails is centos5 dual quad core xenon. If I run a normal solvated simulation, the linux machine runs fine. Elio Cino -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: gromacs with CMAP
Hi, I do not fully understand what you are trying to do, but currently CMAP is only available for the standard amino acid residues present in the rtp-file for the Charmm-forcefield, and the values for the grid are specified in the cmap.itp-file. Do you use something else? /Per 29 jun 2010 kl. 14.45 skrev Da-Wei Li: HI, David, thanks for your advise. I remove the bond angle force and get same result. It is really strange. If I set +5 on all the 24*24 grid, I just get a inverted distribution and if I set 0 on all grid, I will get a uniformed distribution. It is like that 27 regions are force to have zero cmap potential. I cannot attach figure due to size limit the list. I have sent the figure to you directly. best, dawei -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Charmm without CMAP
Hi! You can choose cmap/no cmap when you run pdb2gmx. /Per Skickat från min iPhone 22 jun 2010 kl. 19:24 skrev Sai Pooja saipo...@gmail.com: Hi, I am using gromacs from the git repository which I downloaded 2 days back. Charmm has been implemented in this version. Is it possible to use the Charmm ff without CMAP with it? Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein structure prediction
23 feb 2009 kl. 12.55 skrev Mark Abraham: José Carlos Calvo Tudela wrote: can I use the GROMACS software to get the energy of a protein conformation? Yes, but your question is not well-formed. Only energy differences can have meaning. Up to now I am using TINKER library (analyze program). Is there any similar software in GROMACS? I don't know. If I'm not mistaken, the energy you get from analyse.x program in Tinker is the potential energy for a protein in is current conformation, given a particular force-field. In that case, you might be able to get the same from Gromacs if you do a simulation with 0 steps, ie without any integration, and then look at the potential energy terms in the log file (or do many steps, and look at the energy before the first step) Cheers /Per Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
If atoms are missing in the sidechains of your protein, you can try a program like scwrl3 to rebuild all or some of the sidechains. This will give you complete sidechains in sort of reasonable positions. Cheers /Per 12 aug 2008 kl. 15.04 skrev vivek sharma: Hi David, Thanx a lot again. can you please tell me the criteria or the standards to do such correction or can you suggest some link or tutorial for the same? whether swiss pdb can help in such cases? With Thanx, Vivek 2008/8/12 David van der Spoel [EMAIL PROTECTED] vivek sharma wrote: Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error. .. .. .. ... N-terminus: NH3+ C-terminus: COO- WARNING: atom CE2 not found in residue 270 while adding atom --- Program pdb2gmx, VERSION 3.3.3 Source code file: genhydro.c, line: 304 Fatal error: Atom CE2 not found in residue PHE270 while adding hydrogens --- I tried the same with different force field and water models, but getting the same error again and again. any suggestion will be highly appreciated. You have an incorrect pdb file. An atom is missing. You have to fix it yourself. With thanx, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] (no subject)
Check the information on the gromacs wiki about this: http://wiki.gromacs.org/index.php/Errors#T-Coupling_group_XXX_has_fewer_than_10.25_of_the_atoms Cheers /Per 17 jul 2008 kl. 14.38 skrev [EMAIL PROTECTED]: Hi all I have installed gromacs 3.3.3 in one of my 32 machine fedora core 2. so check i tried to to do speptide tutorial in /usr/local/gromacs/share/gromacs/tutor/speptide But when i m running grompp for position restraint with the command grompp -f pr -o pr -c after_em -r after_em -p speptide i get the following warning WARNING 1 [file aminoacids.dat, line 1]: T-Coupling group Protein has fewer than 10% of the atoms (191 out of 2741) Maybe you want to try Protein and Non-Protein instead? I tried to change SOL with non protein but getting the same warning. is it ok to go further with this warning When i did grompp for full MD with the command grompp -v -f full -o full -c after_pr -p speptide again i m getting the same warning WARNING 1 [file aminoacids.dat, line 1]: T-Coupling group Protein has fewer than 10% of the atoms (191 out of 2741) Maybe you want to try Protein and Non-Protein instead? I tried to change SOL with non protein but getting the same warning. I don't know what to do now and how can i overcome this, if anyone could help me. Thanks ALKA ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] regarding rmsd !!
Check your input/output! In this case it seems you are missing/forgetting the -s flag to specify the name of the tpr-file. /Per 17 jun 2008 kl. 17.07 skrev Anamika Awasthi: Dear All, My protein is simulating for 20 ns and 16 ns has already over, but I want to analyze RMSD and RMSF for this 16 ns simulation, without stopping the running simulation.it was crashed before, so I used tpbconv -f previous.trr -e previous.edr -s previous.tpr -o new.tpr -until 2 then gave the command -- mdrun -s new.tpr -o new.trr -c new.gro -g new.log -e new.edr now job is running now for analysis I am giving this command g_rms new.tpr -f new.trr -o new_rmsd.xvg -xvgr it is giving this output :-) g_rms (-: Option Filename Type Description -s topol.tpr InputStructure+mass(db): tpr tpb tpa gro g96 pdb xml -f new.trr Input Generic trajectory: xtc trr t pdb -f2 traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -n index.ndx Input, Opt. Index file -o new_rmsd.xvg Output xvgr/xmgr file -mirrmsdmir.xvg Output, Opt. xvgr/xmgr file -a avgrp.xvg Output, Opt. xvgr/xmgr file -dist rmsd-dist.xvg Output, Opt. xvgr/xmgr file -m rmsd.xpm Output, Opt. X PixMap compatible matrix file -bin rmsd.dat Output, Opt. Generic data file -bm bond.xpm Output, Opt. X PixMap compatible matrix file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: ps, fs, ns, us, ms, s, m or h -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgr boolyes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -what enum rmsd Structural difference measure: rmsd, rho or rhosc -[no]pbc boolyes PBC check -fit enum rot+trans Fit to reference structure: rot+trans, translation or none -prevint 0 Compare with previous frame -[no]split bool no Split graph where time is zero -skipint 1 Only write every nr-th frame to matrix -skip2int 1 Only write every nr-th frame to matrix -max real -1 Maximum level in comparison matrix -min real -1 Minimum level in comparison matrix -bmax real -1 Maximum level in bond angle matrix -bmin real -1 Minimum level in bond angle matrix -nlevelsint 80 Number of levels in the matrices -ngint 1 Number of groups to compute RMS between --- Program g_rms, VERSION 3.3 Source code file: statutil.c, line: 787 Invalid command line argument: new.tpr --- WHY THIS IS SHOWING THIS ERROR? Thanks in advance Anamika ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] Implicit Solvent Simulations
Hello Una (and everyone else) I'm happy to announce that, while not yet available in cvs, it will very soon be possible to do implicit solvation with Gromacs. I'm have a working implementation almost finished, and are currently running some tests to assure that the code is stable. With any luck we should be able to commit this to cvs in the next month or so :-) Cheers /Per Larsson, PhD student in the Lindahl group 22 maj 2008 kl. 16.13 skrev Una Bjarnadottir: To the Gromacs user community, As of April 2007 it was not possible to do implicit solvent MDs with Gromacs (http://www.gromacs.org/pipermail/gmx-users/2007-April/026849.html). Has this changed since then? Kind regards, Una -- Una Bjarnadottir School of Biomolecular and Biomedical Science Conway Institute UCD Dublin 4, Ireland Phone: +353 1 716 6874, Fax: +353 1 716 6898 Email: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] Help for GNUPlot
Hello! Please note that xmgrace and gunplot are two different programs and as such work in different ways, for example in terms of what types of input and output they expect. The xvg-files that Gromacs produces are indended for xmgrace, and will not work out-of-the-box with gnuplot. There are tons of tutorials on the internet on how to use gnuplot, and I suggest that you start by following a few of those, learning how to first make some simple toy-plots Cheers /Per 6 maj 2008 kl. 15.07 skrev s lal badshah: Dear Mark, Hi ! Currently I tried to install xmgrace but the toolbar menue is not shown on window screen so I am using gnuplot for analysis as I have little know how about unix/linux.Please set to me the following. [EMAIL PROTECTED]:~ cd project [EMAIL PROTECTED]:~/project ls #bfac.pdb.1# conf.pdb genion.log md323.tpr pr.edr topol_A.itp #rmsf.xvg.1# dist.xvg gyrate.xvg md323.trr pr.gro topol_B.itp #topol.top.1# distance.xvg index.ndx md323.xtc pr.log traj.trr #traj.trr.1# em.mdpions.pdbmd323lie.xvg pr.mdp water.pdb 2a5f.pdb em.pdbmd323.edr mdout.mdp pr.tpr bfac.pdb em.tprmd323.gro pe.xvgpr.trr bonds.xvg ener.edr md323.log posre_A.itp rmsf.xvg box.pdbenergy.xvgmd323.mdp posre_B.itp topol.top [EMAIL PROTECTED]:~/project gnuplot G N U P L O T Version 4.2 patchlevel 0 last modified March 2007 System: Linux 2.6.22.5-31-default Copyright (C) 1986 - 1993, 1998, 2004, 2007 Thomas Williams, Colin Kelley and many others Type `help` to access the on-line reference manual. The gnuplot FAQ is available from http://www.gnuplot.info/faq/ Send comments and help requests to [EMAIL PROTECTED] Send bug reports and suggestions to [EMAIL PROTECTED] Terminal type set to 'x11' gnuplot plot rmsf.xvg u 1:2 w ^ expecting 'lines', 'points', 'linespoints', 'dots', 'impulses', 'yerrorbars', 'xerrorbars', 'xyerrorbars', 'steps', 'fsteps', 'histeps', 'filledcurves', 'boxes', 'boxerrorbars', 'boxxyerrorbars', 'vectors', 'financebars', 'candlesticks', 'errorlines', 'xerrorlines', 'yerrorlines', 'xyerrorlines', 'pm3d', 'labels', 'histograms', 'image', 'rgbimage' gnuplot boxes ^ invalid command gnuplot plot lines rmsf.xvg u 1:2 w undefined variable: lines gnuplot plot gyrate.xvg undefined variable: gyrate gnuplot plot gyrate.xvg ^ Bad data on line 9 gnuplot Regards, Lal badshah Send instant messages to your online friends http://uk.messenger.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] results of energy minimization
Hello! Check out http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small.2C_or_no_change_in_energy._Converged_to_machine_precision.2C_but_not_to_the_requested_precision Cheers /Per 12 mar 2008 kl. 11.58 skrev s lal badshah: Dear gromacs experts, I have run the energy minimization of a protein.With the tail command it shows the following results: [EMAIL PROTECTED]:~/protein tail -15 md.log NS-Pairs 94.365846 1981.68276620.0 Reset In Box 0.5693855.124465 0.1 Shift-X 0.5693103.415860 0.0 CG-CoM0.1907855.532765 0.1 Bonds 0.394530 16.964790 0.2 Angles0.253320 41.291160 0.4 Propers 0.0098552.256795 0.0 RB-Dihedrals 0.086835 21.448245 0.2 --- Total 9893.632954 100.0 --- NODE (s) Real (s) (%) Time: 15.000 15.000100.0 Finished mdrun on node 0 Wed Mar 12 12:50:59 2008 I have check the em.log file, which shows the following data: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = -1.9742134e+21 Maximum force = 4.1648520e+06 on atom 1934 Norm of force = 5.6557945e+06 Is the energy minimization finished or not? when I use the top command the values fluctuates.As there any specific value or notation below the command name from which I know that energy minimization is running or finished.As in amber software the word sander is written below the command when check with top .Here X is written. Regards, Lal badshah. Send instant messages to your online friends http://uk.messenger.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] Step size too small
Hello! Check out http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small. 2C_or_no_change_in_energy._Converged_to_machine_precision. 2C_but_not_to_the_requested_precision Cheers /Per 17 aug 2007 kl. 18.28 skrev Sheyore Omovie: Dear gmx-users, I have 2 molecules in a box, as usual pdb2gmx saw them as one. i edited the .top file to remove the bonds created between the two molecules, I also added a distance restraint btw the molecules. (The 2 structures have been separately minimized). However, I get the ff message for EM run: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.0246325e+20 Maximum force =inf on atom 1 Norm of force =inf I would appreciate any advice on how to fix this. Rgds John See what you’re getting into…before you go there See it! ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] stepsize too small
Hello! There are many discussions on the maillist about this... In short, if all you want to do is normal md, it should be ok to just proceed with that. Just check that your potential energy is negative and everything should fine. Otherwise, recompiling Gromacs to use double precision might get you a bit lower in energy, or change integrator to see if you get any lower. Cheers /Per 13 aug 2007 kl. 20.08 skrev burkhard rammner: Hi, This is the first time I`m using gromacs. That`s why I`m having a beginners`question. I tried to do an energy minimization, but after 45 steps this message appears and I know that the following lines have led to questions before: Stepsize too small (9.09769e-007 nm)Converged to machine precision, but not to the requested precision (1000) I`m using single precision windows compiled gromacs. I know, I have to change whatever parameter, but so far I didn`t succeed. This is the mdp file: integrator= steep emtol = 1000 emstep = 0.01 nsteps= 200 nstenergy = 10 nstxtcout= 10 xtc_grps= Protein energygrps = Protein nstlist = 5 ns_type = simple rlist = 1.0 coulombtype= cut-off rcoulomb = 1.0 rvdw= 1.0 constraints= none pbc = no So, what`s wrong here? What do I have to change? Many thanks for help! Burkhard ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] problem with writing energies
Hello! Are you out of disk-space? Cheers /Per 2 aug 2007 kl. 08.49 skrev aneesh chandran: Hello Users I am using gromacs 3.3 with g43a1 force field. I am running a MD without any position restraints. After around 770 ps system stoped running with an error could not write energies. what could be the problem? waiting for an early reply Thanks in advance with regards Aneesh following is the part of log file Energies (kJ/mol) G96Bond G96AngleProper Dih. Improper Dih. LJ-14 2.12163e+033.41254e+031.42482e+031.04269e+03 4.50126e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 2.43870e+041.06622e+05 -7.33872e+05 -9.53957e+04 -6.89807e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 1.26392e+05 -5.63415e+053.00768e+021.69426e+02 Step Time Lambda 386000 772.60.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.048496 2033 2034 0.013339 After LINCS 0.26269271 0.03 Energies (kJ/mol) G96Bond G96AngleProper Dih. Improper Dih. LJ-14 2.21432e+033.34757e+031.50922e+039.45264e+02 4.92081e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 2.46610e+041.04777e+05 -7.32472e+05 -9.54459e+04 -6.89972e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 1.26415e+05 -5.63557e+053.00823e+02 -3.26087e+01 Step Time Lambda 386100 772.200010.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.060718968969 0.014659 After LINCS 0.15602605 0.02 --- Program mdrun, VERSION 3.3 Source code file: enxio.c, line: 343 Fatal error: could not write energies --- following is my input file integrator= md dt= 0.002 nsteps= 125000 nstxout = 100 nstvout = 100 nstlog= 100 nstenergy = 100 nstxtcout = 0 energygrps= protein sol MG2+ nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 pbc = xyz tcoupl= berendsen tc-grps = protein sol MG2+ tau_t = 0.1 0.1 MG2+ ref_t = 300 300 300 Pcoupl= berendsen Pcoupltype= isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300 gen_seed = 173529 constraints = hbonds Unlimited freedom, unlimited storage. Get it now ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] error in pdb2gmx step
Check you pdb file and see if the chain identifier A occurs at different places in the file. Pdb2gmx expects a chain to be continous, and if it isn't, it gets confused. If you have several chains, rename them accordingly. Cheers /Per Annie Albin wrote: Dear all, I faced a problem in the pdb2gmx step as i got this following error message, Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 908, atom 7013) As I'm pretty new to this field. I'm finding it difficult to troubleshoot. Any suggestions would be of great help. Thank you, Annie Albin. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Per Larsson PhD Student Stockholm Bioinformatics Center +46 (0) 8 55378577 +46 (0) 733 461467 [EMAIL PROTECTED] www.sbc.su.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
