Hi Ravi, I had a similar problem to yours when I was dealing with simulation of a peptide channel. I had the crystal structure of the channel consisting of crystal water molecules and the peptide channel. I energy minimized the system. Although nothing seems to be overlap, energy minimization crashed. After that I decided to put each water molecule into the channel one by one, and did energy minimization after each water molecule. If the energy minimization did not crash, I continued adding another water molecule. If it crashed I changed the location of the last water molecule in the channel. But I am afraid you have much more water molecules than mine. I had more or less 100 water molecules within the channel, and also note that I had not any ions in the system.
Regards On Thu, Apr 8, 2010 at 9:13 AM, <gmx-users-requ...@gromacs.org> wrote: > 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: energy minimization in charged systems (Dallas B. Warren) > 2. Simulating a metal slab (radhika jaswal) > 3. Re: Simulating a metal slab (Mark Abraham) > 4. Re: position_restraint anfd full Dynamics and berendsen Nose > hoover Thermostat (shahid nayeem) > 5. Re:Re: g_nmeig_d error:cannot allocate region > (sarbani chattopadhyay) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 08 Apr 2010 15:22:53 +1000 > From: "Dallas B. Warren" <dallas.war...@pharm.monash.edu.au> > Subject: RE: [gmx-users] energy minimization in charged systems > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <89907ea1dcfb7548a431c13a270f9dd509b82...@prk-exch-01.vcp.local> > Content-Type: text/plain; charset=iso-8859-1 > > What are the atoms that are causing the problems actually doing, where are > they located etc? > > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@pharm.monash.edu.au > +61 3 9903 9167 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Ravi Bhadauria > Sent: Thursday, 8 April 2010 3:11 PM > To: gmx-users@gromacs.org > Subject: [gmx-users] energy minimization in charged systems > > Hi all, > > I am trying to simulate a electroosmotic flow in a nanochannel. System > consists of water + (Cl-) ions in a channel confined of silicon <111> walls. > I start with taking water as only solvent, equilibrating the system for > about 12-15 ps (gmxcheck runs clean), and then use genion to insert (Cl-) > ions. Walls are charged appropriately to maintain electro-neutrality in the > system. The problem is with Energy minimization after inserting ions using > steep algorithm (haven't turned on the electric field yet). I am getting an > error like this: > > t = 0.038 ps: Water molecule starting at atom 2569 can not be settled. > Check for bad contacts and/or reduce the timestep. > Wrote pdb files with previous and current coordinates > > and > > Steepest Descents converged to machine precision in 88 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = 1.75456106043895e+06 > Maximum force = 1.07111309902475e+11 on atom 4898 > Norm of force = 1.48772609239112e+09 > > If it were only couple of such molecules, I could have removed them easily > from the gro file. The problem is twofold, there are around 10 molecules > which give this error message, plus even after removal of these molecules, > energy minimization results in the same error on different sets of > molecules. I have tried a number of ways to tackle this including tuning the > time step. Is there any way to avoid this? Any help would be appreciated. > > Thanks in advance. > > -- > Ravi Bhadauria > > > ------------------------------ > > Message: 2 > Date: Thu, 8 Apr 2010 11:17:15 +0530 (IST) > From: radhika jaswal <jaswalradh...@yahoo.co.in> > Subject: [gmx-users] Simulating a metal slab > To: gmx-users@gromacs.org > Message-ID: <109124.71315...@web94806.mail.in2.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > Hii Everybody... > > > > I want to simulate a Titanium Oxide slab of approx. 8-9 molecules in > length and 4-5 molecules wide just as to mimic a rigid metal slab for > further interaction studies. Can gromacs library support this and how I > can do that... > > All suggestions are welcome. > > > > Thanks > > > > Radhika > > > > Send free SMS to your Friends on Mobile from your Yahoo! Messenger. > Download Now! http://messenger.yahoo.com/download.php > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100408/4e834c1c/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Thu, 08 Apr 2010 15:54:24 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] Simulating a metal slab > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4bbd6f90.7080...@anu.edu.au> > Content-Type: text/plain; charset=UTF-8; format=flowed > > On 8/04/2010 3:47 PM, radhika jaswal wrote: > > Hii Everybody... > > > > I want to simulate a Titanium Oxide slab of approx. 8-9 molecules in > > length and 4-5 molecules wide just as to mimic a rigid metal slab for > > further interaction studies. Can gromacs library support this and how I > > can do that... > > Yes, in principle. You will need a force field that supports such > interactions, and GROMACS does not come with any. Your first place to > look should be in the published literature for other simulations of such > materials and such slabs. Don't assume GROMACS is the best tool for the > task. > > Mark > > > ------------------------------ > > Message: 4 > Date: Thu, 8 Apr 2010 11:27:37 +0530 > From: shahid nayeem <msnay...@gmail.com> > Subject: Re: [gmx-users] position_restraint anfd full Dynamics and > berendsen Nose hoover Thermostat > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <o2mea6f7fbe1004072257yedd75eebn7c8f2e714d14a...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Please see the following pr.mdp and full.mdp > pr.mdp > > > cpp = /usr/bin/cpp > > define = -DPOSRES > > constraints = all-bonds > > integrator = md > > dt = 0.002 ; ps ! > > nsteps = 50000 ; total 100 ps. > > nstcomm = 1 > > nstxout = 500 > > nstvout = 1000 > > nstfout = 0 > > nstlog = 10 > > nstenergy = 10 > > nstlist = 10 > > ns_type = grid > > rlist = 1.0 > > rcoulomb = 1.0 > > rvdw = 1.0 > > ; Berendsen temperature coupling is on in two groups > > Tcoupl = berendsen > > tc-grps = Protein Non-protein > > tau_t = 0.1 0.1 > > ref_t = 500 500 > > ; Energy monitoring > > energygrps = Protein Non-protein > > ; Pressure coupling is not on > > Pcoupl = no > > tau_p = 0.5 > > compressibility = 4.5e-5 > > ref_p = 1.0 > > ; Generate velocites is on at 500 K. > > gen_vel = yes > > gen_temp = 500.0 > > gen_seed = 173529 > > full.mdp > > cpp = /usr/bin/cpp > > constraints = all-bonds > > integrator = md > > dt = 0.002 ; ps ! > > nsteps = 50000000 ; total 100000 ps. > > nstcomm = 1 > > nstxout = 5000 > > nstvout = 40000 > > nstfout = 0 > > nstlog = 100 > > nstenergy = 100 > > nstlist = 10 > > ns_type = grid > > rlist = 1.0 > > rcoulomb = 1.0 > > rvdw = 1.0 > > ; Berendsen temperature coupling is on in two groups > > Tcoupl = berendsen > > tc-grps = Protein Non-protein > > tau_t = 0.1 0.1 > > ref_t = 500 500 > > ; Energy monitoring > > energygrps = Protein Non-protein > > ; Isotropic pressure coupling is now on > > Pcoupl = berendsen > > Pcoupltype = isotropic > > tau_p = 0.5 > > compressibility = 4.5e-5 > > ref_p = 1.0 > > ; Generate velocites is off at 500 K. > > gen_vel = no > > gen_temp = 500.0 > > gen_seed = 173529 > > Please tell me why protein shows unfolding in very first frame. > > msnayeem > > > > > > > > On 4/7/10, Mark Abraham <mark.abra...@anu.edu.au> wrote: > > > > On 7/04/2010 9:08 PM, shahid nayeem wrote: > > > >> Dear users > >> Please let me know some basic question. I am sorry if I am asking a > >> silly question. > >> a) While simulating a protein thermal unfolding at high temperature say > >> 500K should I run position restraint dynamics at 500k or at 298K. I am > >> doing 100ps position restraint dynamics at 500k. Am I right in doing so. > >> > > > > The usual purpose of position restrained MD is to allow the system to > > achieve close to the ensemble desired for the start of the simulation > > without perturbing the initial structure. > > > > b) While using Berendsen thermostat, how to select a value of tau_t and > >> how does it affects simulation output. The same question for NoseHoover > >> thermostat. > >> > > > > Start by reading the GROMACS manual sections. > > > > c) After completing the 100ns simulation when I view the .xtc file in > >> VMD I find that alpha helix of the protein is unfolded in very first > >> frame collected at 10ps interval and reduced by trjconv at 50ps > >> interval. Is it possible. If not then where I am wrong. > >> I did Steepest descent minimization, then 100ps position restraint > >> Dynamics at 500K and then 100ns full dynamics at 500k. > >> > > > > 10ps would be very fast for a lengthy helix to unfold, however you've > > deliberately taken your force field out of the zone where it was > > parameterized, so we can't really infer anything about its behaviour. You > > could also have a broken model physics in your .mdp file, but we can't > know > > about that. > > > > The real lesson here is not to do a lengthy simulation without looking at > > the early and ongoing results. > > > > Mark > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/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 > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100408/40ced543/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: 8 Apr 2010 06:06:40 -0000 > From: "sarbani chattopadhyay" <sarbani_...@rediffmail.com> > Subject: [gmx-users] Re:Re: g_nmeig_d error:cannot allocate region > To: <gmx-users@gromacs.org> > Message-ID: <20100408060640.59473.qm...@f5mail-236-240.rediffmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi, > I had checked and found that gromacs has been compiled in 64 bit mode. > However still I am getting this error with "g_nmeig_d " command which says > g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error > code=12) > *** error: can't allocate region > > > I am running this on a 8 node machine,each with 2GB of RAM ( g_nmeig_d > runs on a single node). > > Is it required to increase the RAM of 1 node to get rid of this error? > Any suggestion will be very helpful. > Thanking You, > Sarbani > > > > On Tue, 02 Mar 2010 20:01:51 +0530 wrote > > > > > > > Hi, > > > > > > The allocation that causes the error should allocate about 3 GB. > > > My guess is that you compiled Gromacs in 32bit mode, whereas 64bit mode > > > is required for allocation of more than 2 GB. > > > > > > Berk > > > > > > Date: Tue, 2 Mar 2010 13:35:58 +0000 > > > To: gmx-users@gromacs.org > > > From: sarbani_...@rediffmail.com > > > Subject: [gmx-users] g_nmeig_d error: can't allocate region > > > > > > Hi, > > > > > > I am trying to do normal mode analysis on a protein having 6398 atoms in > vaccum. > > I tried to energy minimize the structure using steepest descent, followed > by "l-bfgs" > minimization. the .mdp file I used is > > define = -DFLEXIBLE > > constraints = none > integrator = l-bfgs > tinit = 0 > nsteps = 15000 > nbfgscorr = 50 > emtol = .001 > emstep = 0.1 > gen_vel = yes > gen-temp = 300 > nstcomm = 1 > ; NEIGHBORSEARCHING PARAMETERS > ; nblist update frequency > nstlist = 0 > ; ns algorithm (simple or grid) > ns-type = simple > ; Periodic boundary conditions: xyz (default), no (vacuum) > or full (infinite systems only) > pbc = no > rlist = 0 > domain-decomposition = no > ; OPTIONS FOR ELECTROSTATICS AND VDW > ; Method for doing electrostatics > coulombtype = Cut-Off > rcoulomb-switch = 0 > rcoulomb = 0 > ; Dielectric constant (DC) for cut-off or DC of reaction field > epsilon-r = 1 > ; Method for doing Van der Waals > vdw-type = Cut-off > ; cut-off lengths > rvdw-switch = 0 > rvdw = 0 > > > > after running the 15000 steps the Fmax was:> > Low-Memory BFGS Minimizer converged to Fmax < 0.001 in 10197 steps > > Potential Energy = -8.26391832320506e+04 > > Maximum force = 9.37558560558845e-04 on atom 4562 > > Norm of force = 2.24887722104890e-04 > > Again the "l-bfgs" minimization was run using the same .mdp file( with > emtol = > 0.000001)> > the output was' > > > > > > Low-Memory BFGS Minimizer converged to Fmax < 1e-06 in 4143 steps > > > > > > Potential Energy = -8.26391832324998e+04 > > > > > > Maximum force = 9.67927896882578e-07 on atom 3271 > > > > > > Norm of force = 1.70637151528245e-07 > > > > > > > > > > > > > > > > > > > > > > > > After this I prepared the "nm.mdp " file for NMA, where I used exactly the > same parameters > > > > > > as the ones used in lbfgs energy minimization( with integrator = nm) > > > > > > > > > > > > the commands that were used were: > > > > > > grompp_d -f new_nm.mdp -t new_lbfgs_2.trr -c new_lbfgs_2.gro -o new_nm.tpr > -zero -p > > > > > > ../topol.top > > > > > > > > > > > > nohup mdrun_d -v -s new_nm.tpr -deffnm new_nm -mtx new_nm.mtx & > > > > > > > > > > > > > > > > > > "nohup.out" had the following message: > > > > > > Non-cutoff electrostatics used, forcing full Hessian format.Allocating > Hessian > > > > > > memory...starting normal mode calculation 'Protein'6398 steps.Maximum > force: 9.67928e-07 > > > > > > > > > > > > > > > > > > The run ended successfully: > > > > > > > > > > > > Then i used the command > > > > > > g_nmeig_d -f new_nm.mtx -s new_nm.tpr -ol eigenvalue.xvg -v eigenvector.trr > > > > > > > > > > > > I get the following error: > > > > > > Reading file new_nm.tpr, VERSION 4.0.7 (double precision) > > > > > > Reading file new_nm.tpr, VERSION 4.0.7 (double precision) > > > > > > Reading double precision matrix generated by Gromacs VERSION 4.0.7 > > > > > > Full matrix storage format, nrow=19194, ncols=19194 > > > > > > > > > > > > Diagonalizing to find vectors 1 through 50... > > > > > > g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error > code=12) > > > > > > *** error: can't allocate region > > > > > > *** set a breakpoint in malloc_error_break to debug > > > > > > > > > > > > I am not being able to understand the problem. the computer has a 16gb > memory > > > > > > > > > > > > > > > > > > > > > > > > If I use different parameters in the nm.mdp file as > > > > > > > > > > > > rlist = 1.5 > > > > > > domain-decomposition = no > > > > > > ; OPTIONS FOR ELECTROSTATICS AND VDW > > > > > > ; Method for doing electrostatics > > > > > > coulombtype = switch > > > > > > rcoulomb-switch = 1 > > > > > > rcoulomb = 1.2 > > > > > > ; Dielectric constant (DC) for cut-off or DC of reaction field > > > > > > epsilon-r = 1 > > > > > > ; Method for doing Van der Waals > > > > > > vdw-type = switch > > > > > > ; cut-off lengths > > > > > > rvdw-switch = 1 > > > > > > rvdw = 1.2 > > > > > > > > > > > > > > > > > > then i get the message :Maximum force: 3.14171e+03 > > > > > > 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. > > > > > > > > > > > > > > > > > > I am sorry to post such a lengthy query, but I have no clue about the root > of the problem. > > > > > > Any suggestion will be of great help. > > > > > > Thanks in advance, > > > > > > Sarbani. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100408/a584f68b/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 72, Issue 36 > ***************************************** > -- Ozge Engin ★☆
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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