Dear Mark, Thanks a lot for the reply and highlighting the cause of error that I was facing. Still can it be possible to overcome the same error with the available facility.
Pavan Payghan On Thu, Apr 26, 2012 at 9:55 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. Free Energy calcualtions (Sai Kumar Ramadugu) > 2. How to choose two atoms at the same time, using g_select > selection.dat (mu xiaojia) > 3. Re: How to choose two atoms at the same time, using g_select > selection.dat (Justin A. Lemkul) > 4. Re: why it is so slow in Blue gene? (Mark Abraham) > 5. Fwd: Error: coordinate file does not match with the topology > file (Mark Abraham) > 6. Re: How to increase the ratio of cell size to constrain > length per error message (Mark Abraham) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 25 Apr 2012 16:05:05 -0500 > From: Sai Kumar Ramadugu <sramad...@gmail.com> > Subject: [gmx-users] Free Energy calcualtions > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <cao6uzqupcxncot6qbkwlrrrifpk2y3cicffts7+fwyyjrb0...@mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Gromacs Users, > I want to mutate a glutamate in my protein to alanine in presence of a > ligand. > With glutamate, the protein charge is -3. To neutralize the system, I added > 3K+ ions. > Now when I mutate GLU to ALA, the charge in state_B will be +1 (protein -2 > + 3K+). > > Right now I'm in the charge part of the mutation. Once this is successful, > I will include the VDW mutation too. > > I have added the mutation details of Glu to Ala residue in the topology in > [atoms], [bonds], [angles] and [dihedrals] sections. > > After I run the grompp command, the result says that my State_B topology > has +1 charge since I am not including mutation of one K+ ion to neutral K+ > ion. > How can I mutate 1 particular K+ to K atom and subsequently to a dummy > atom? Since I'm using OPLS force field, we have ions.itp to be used in the > topology file, changing one K+ is making it troublesome for me to implement > in the topology file. > Any suggestions are helpful. > > Thanks for your time. > > Regards > Sai > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120425/a8a8f0b1/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Wed, 25 Apr 2012 20:19:22 -0500 > From: mu xiaojia <muxiaojia2...@gmail.com> > Subject: [gmx-users] How to choose two atoms at the same time, using > g_select selection.dat > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <cabsftfqree885zmhdqq6n2qrjcko2c-sdupot_utjbxkkyo...@mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear gmx users, > > I may have a silly question, how to make a group of two atoms from the same > molecule? > > e.g, I want to make an "HN" group of both H and N from my 2nd residue, > > I know for single one, commands in *.dat file is like: > > nameN = resnr 2 and name N; > nameH = resnr 2 and name H; > > nameN; > nameH; > > I guess "merge" or "plus" might be helpful,I think it should be done > something like: "nameN_H = resnr 2 and name N ?? resnr 2 and name H", so it > is an intramolecular combination between N and H; it shouldn't be done > afterwards, otherwise it would be an intermolecular combination. > > Thanks very much! g_select is really powerful, and hopefully there would be > more examples. > > Jia > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120425/87d7ac37/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Wed, 25 Apr 2012 21:24:21 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] How to choose two atoms at the same time, > using g_select selection.dat > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4f98a3c5.8040...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 4/25/12 9:19 PM, mu xiaojia wrote: > > Dear gmx users, > > > > I may have a silly question, how to make a group of two atoms from the > same > > molecule? > > > > e.g, I want to make an "HN" group of both H and N from my 2nd residue, > > > > I know for single one, commands in *.dat file is like: > > > > nameN = resnr 2 and name N; > > nameH = resnr 2 and name H; > > > > nameN; > > nameH; > > > > I guess "merge" or "plus" might be helpful,I think it should be done > something > > like: "nameN_H = resnr 2 and name N ?? resnr 2 and name H", so it is an > > intramolecular combination between N and H; it shouldn't be done > afterwards, > > otherwise it would be an intermolecular combination. > > > > Thanks very much! g_select is really powerful, and hopefully there would > be more > > examples. > > > > g_select is more suited for complex groups that are dynamic or otherwise > based > on geometric criteria. If you're trying to make a simple group that > consists of > 2 atoms, make_ndx is easier, and using a plain text editor will be > easiest, i.e.: > > [ my_group ] > 1 2 > > -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 > > ======================================== > > > ------------------------------ > > Message: 4 > Date: Thu, 26 Apr 2012 14:04:49 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] why it is so slow in Blue gene? > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4f98c961.9030...@anu.edu.au> > Content-Type: text/plain; charset=UTF-8; format=flowed > > On 25/04/2012 3:24 PM, Albert wrote: > > hello: > > > > it is blue gene P. And the gromacs is single precision in the > > cluster. Getting Loaded...And the administrator told me that I have to > > use the multiples of 32 in the bg_size parameter. The number specified > > in "-np" should be 4 times bg_size. > > Yes, but your system is too small to make use of 128 processors. Also, > get rid of -launch and -nt from your command line, since they do nothing. > > > It is even slower than my own workstation with 16 core......... > > > > > > > > > > here is the log file I get: > > No, that's the stdout file. Look at the end of the .log file. > > > > > -------------log---------------- > > Reading file npt_01.tpr, VERSION 4.5.5 (single precision) > > Loaded with Money > > > > Will use 112 particle-particle and 16 PME only nodes > > This is guaranteed to lead to woeful performance with your .mdp > settings, but you will have to look towards the beginning of the .log > file to find out why mdrun selected this. Odds are good that your system > size is so small that the minimum particle-particle cell size > (constrained by rcoulomb) doesn't give mdrun any good options that use > all the processors. You'd likely get better raw performance with twice > the number of atoms or half the number of processors. > > Mark > > > This is a guess, check the performance at the end of the log file > > Making 3D domain decomposition 4 x 4 x 7 > > starting mdrun 'GRowing Old MAkes el Chrono Sweat' > > 500000 steps, 500.0 ps. > > step 0 > > vol 0.64! imb F 16% pme/F 0.22 step 100, will finish Wed Apr 25 > > 18:28:06 2012 > > vol 0.65! imb F 17% pme/F 0.21 step 200, will finish Wed Apr 25 > > 18:09:54 2012 > > vol 0.67! imb F 18% pme/F 0.21 step 300, will finish Wed Apr 25 > > 18:03:12 2012 > > vol 0.69! imb F 18% pme/F 0.21 step 400, will finish Wed Apr 25 > > 17:58:25 2012 > > vol 0.67! imb F 19% pme/F 0.21 step 500, will finish Wed Apr 25 > > 17:55:26 2012 > > vol 0.68! imb F 19% pme/F 0.22 step 600, will finish Wed Apr 25 > > 17:53:31 2012 > > vol 0.68! imb F 19% pme/F 0.22 step 700, will finish Wed Apr 25 > > 17:51:57 2012 > > vol 0.68! imb F 19% pme/F 0.22 step 800, will finish Wed Apr 25 > > 17:50:32 2012 > > vol 0.68! imb F 20% pme/F 0.22 step 900, will finish Wed Apr 25 > > 17:49:14 2012 > > vol 0.67! imb F 21% pme/F 0.22 step 1000, will finish Wed Apr 25 > > 17:48:13 2012 > > vol 0.68! imb F 20% pme/F 0.22 step 1100, will finish Wed Apr 25 > > 17:47:28 2012 > > vol 0.67! imb F 21% pme/F 0.22 step 1200, will finish Wed Apr 25 > > 17:46:50 2012 > > vol 0.67! imb F 21% pme/F 0.22 step 1300, will finish Wed Apr 25 > > 17:46:15 2012 > > > > > > > > On 04/24/2012 06:01 PM, Hannes Loeffler wrote: > >> On Tue, 24 Apr 2012 15:42:15 +0200 > >> Albert<mailmd2...@gmail.com> wrote: > >> > >>> hello: > >>> > >>> I am running a 60,000 atom system with 128 core in a blue gene > >>> cluster. and it is only 1ns/day.... here is the script I used for > >> You don't give any information what exact system that is (L/P/Q?), if > >> you run single or double precision and what force field you are using. > >> But for a similar sized system using a united atom force field in > >> single precision we find about 4 ns/day on a BlueGene/P (see our > >> benchmarking reports on > >> http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx). I would > >> expect a run with the CHARMM 27 force field in double precision to be > >> roughly 3 times slower. We found scaling to 128 cores to be > >> reasonably good. Also, check our report for problems when compiling > >> with higher optimisation. > >> > >> Hannes. > > > > > > ------------------------------ > > Message: 5 > Date: Thu, 26 Apr 2012 14:13:06 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: [gmx-users] Fwd: Error: coordinate file does not match with > the topology file > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4f98cb52.1060...@anu.edu.au> > Content-Type: text/plain; charset="iso-8859-1" > > Please do not make unsolicited general GROMACS inquiries to private > email addresses. The mailing lists exist for these kinds of purposes. > > On point, you cannot be helped unless you provide the command lines that > you used and describe the objectives you were trying to achieve. > Whatever changes you make to one of the coordinate and .top file must be > matched in the other. > > Mark > > -------- Original Message -------- > Subject: Error: coordinate file does not match with the topology > file > Date: Wed, 25 Apr 2012 02:05:45 +0800 (SGT) > From: sonali shinde <shindesonal...@yahoo.co.in> > Reply-To: sonali shinde <shindesonal...@yahoo.co.in> > To: mark.abra...@anu.edu.au <mark.abra...@anu.edu.au> > > > > > ----- Forwarded Message ----- > *From:* sonali shinde <shindesonal...@yahoo.co.in> > *To:* vini k <vineetha_mand...@yahoo.co.in> > *Sent:* Monday, 23 April 2012 6:48 PM > *Subject:* Error: coordinate file does not match with the topology file > > Dear Sir, > I am a user of gromacs 4.0 for molecular dynamic study of > a protein molecule. I have generated trajectory file before using the > same commands that I use now. Recently I am suffering some problem using > Gromacs , my coordinate file does not matches with the topology file.I > have attached the pdb file protein, .gro and .top file . I have > encountered same error a number of times with three different > proteins.Please suggest the answer for the same. > Thanking you. > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120426/23d33012/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Thu, 26 Apr 2012 14:24:53 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] How to increase the ratio of cell size to > constrain length per error message > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4f98ce15.4040...@anu.edu.au> > Content-Type: text/plain; charset="iso-8859-1" > > On 25/04/2012 6:28 AM, PAVAN PAYGHAN wrote: > > > > Dear Gromacs Users, > > > > I am using gromacs version is 4.5.3.and running my jobs on single node > > with 8 cores. > > > > I have two different systems which contain about 425000 atoms (protein > > + Lipid +SOL) one with bound ligand > > > > and another one unbound protein.I have successfully reached up to > > NPT equilibration run step, > > > > It is a poor idea to do equilibration with Parinello-Rahman, which is > unstable when the system is not already close to equilibrium. For some > reason people still do it, despite at least a post per week on this list > suggesting against it, and a warning in the manual. Use Berendsen to fix > the density, then equilibrate further with P-R to get the right ensemble. > > > now I want to continue the same for production run. Without ligand I > > am able to run successfully But the same system with ligand is > > crashing with following error- > > > > D D cell 1 0 0 could only obtain 1520 of the 1521 atoms that are > > > > are connected via constraints from the neighbouring cells > > > > This probably means your constraint length are too long > > > > compared to the domain decomposition cell size. > > > > Decrease the number of domain decomposition grid cells or lincs_order. > > > > I'd rather expect your system was blowing up because of the above issue. > Perhaps the suggestion in the error message is not as complete as could > be desired - you have so many atoms per processor that the constraint > length would normally be tiny with respect to the cell size. So I think > the things you have tried below are rearranging the deck chairs on the > Titanic. > > Mark > > > Accordingly following the suggestions given in the error I tried to > > solve it with > > > > Following log file and changed, > > > > 1.1. -rcon > > > > Estimated maximum distance required for p-lincs was 0.877 thus > > I increased it to 0.900 > > > > then it thrown another error. > > > > The initial cell size (0.877) is smaller than the cell size limit > > (0.900) > > > > > > 2 .Then I tried to increase the --dds and --rdd from original values > > of 1.25 and 0.623 to 1.30 and 0.670 respectively. > > > > But it does not help and ended with run crash. > > > > /*What I did was logical or I did it wrongly?*/ > > > > /*Now can anyone please suggest me the appropriate way to deal with > > the problem mentioned above? */ > > > > As I want the continuation of the same run without altering the output > > after change in the parameters (As I have to compare the output with > > unbound protein run thus can't afford change in output with change in > > parameters) > > > > I know that I need to change some of the parameters in .mdp file such as > > > > fourierspacing from 0.16 to 0.12 and on the contrary increase the > > pme_order from say 4 to 6. > > > > /*But as asked above by doing so the output will not or will be the > > exact continuation run?*/ > > > > /*How to increase the ratio of cell size to constrain length per error > > message?*/ > > > > /*If any better way of doing so without changing the output please > > suggest,*/ > > > > I am suffering from the same problem since long, > > > > Please help me .Please see the mdp file for the reference. > > > > integrator = md > > > > nsteps = 10000000 > > > > dt = 0.002 ; 2 fs > > > > > > ; Output control > > nstxout = 1000 ; > > nstvout = 1000 ; > > nstxtcout = 1000 ; > > > > nstenergy = 1000 ; > > > > nstlog = 1000 ; > > ; Bond parameters > > continuation = yes ; Restarting after NPT > > constraint_algorithm = lincs ; holonomic constraints > > constraints = all-bonds ; all bonds (even heavy atom-H > > bonds) > > lincs_iter = 1 ; accuracy of LINCS > > lincs_order = 4 > > > > ; Neighborsearching > > ns_type = grid > > nstlist = 5 > > > > rlist = 1.2 > > rcoulomb = 1.2 > > rvdw = 1.2 > > ; Electrostatics > > coulombtype = PME > > pme_order = 4 > > fourierspacing = 0.16 > > tcoupl = Nose-Hoover > > tc-grps = Protein P SOL_NA_CL ; > > tau_t = 0.5 0.5 0.5 > > ref_t = 323 323 323 group, in K > > ; Pressure coupling is on > > pcoupl = Parrinello-Rahman ; > > > > pcoupltype = semiisotropic > > tau_p = 2.0 ; time > > ref_p = 1.0 1.0 ; reference > > compressibility = 4.5e-5 4.5e-5 ; > > > > ; Periodic boundary conditions > > pbc = xyz ; 3-D PBC > > > > ; Dispersion correction > > DispCorr = EnerPres ; account for cut-off vdW scheme > > > > ; Velocity generation > > gen_vel = no > > > > Thanking in Advance > > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120426/7b577a01/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 96, Issue 189 > ****************************************** >
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