On Thu, Apr 23, 2009 at 11:55 AM, <[email protected]> wrote:
> Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: np command with GROMACS 4.0.4 (Vitaly V. Chaban) > 2. Re: RMSD of Aminoacids (Mark Abraham) > 3. problem in topology file of protein-lipid bilayer system for > grompp (nitu sharma) > 4. validating gromacs installation 4.0.4 ( Y. U. Sasidhar ) > 5. Re: problem in topology file of protein-lipid bilayer system > for grompp (Mark Abraham) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 22 Apr 2009 22:36:51 +0200 > From: "Vitaly V. Chaban" <[email protected]> > Subject: [gmx-users] Re: np command with GROMACS 4.0.4 > To: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > If seems in the gmx versions above 4.0 '-np' is not used. If I am not > mistaken you should just point out the number of nodes in your queueing > system while submitting the job. > > Vitaly > > > > I am trying to do my position restrained dynamic simulation on GROMACS > > 4.0.4, and I want to use 4 nodes on the cpu cluster available at my > campus; > > I typed in the following grompp command: > > > > grompp -np 4 -f pr.mdp -c BR6_em.pdb -p BR6.top -o BR6_pr.tpr -n prot.ndx > > -maxwarn 10 > > > > and it gave me the response that -np is an invalid command. > > > > How do I get grompp to rec. that I want to use 4 processors? Because my > > job > > script where I have specified 4 nodes, will not work unless I have np 4 > > included in my grompp. I did see that it works with GROMACS 3.3.3...but > is > > there a way to do it with 4.0.4? > > > > Thanks so much! > > > > Halie Shah > > University of Houston, TX U.S. > > Briggs Lab > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090422/363187da/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Thu, 23 Apr 2009 10:04:36 +1000 > From: Mark Abraham <[email protected]> > Subject: Re: [gmx-users] RMSD of Aminoacids > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Andy Torres wrote: > > Hi, I'm trying to compare two proteins with the same number of > > aminoacids with g_confrms, and it works all right, but it gives me the > > RMSD of the hole protein, and I need the distances (or deviations) of > > each aminoacid. I know this data shoul be there, but I don't know how to > > get it (I've got the mean structure of each protein, calculated with > > g_rmsf, but this data is not fitted each other) > > Have a look at g_confrms -h. Probably with the right index groups > constructed you can fit with one group and observe the RMSD with another. > > Mark > > > ------------------------------ > > Message: 3 > Date: Thu, 23 Apr 2009 10:31:10 +0530 > From: nitu sharma <[email protected]> > Subject: [gmx-users] problem in topology file of protein-lipid bilayer > system for grompp > To: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Justin > > I am doing simulation of membrane protein .I > follow your tutorial for that I think its perfect for that. But I am > getting > problem in doing inflategro step, I alredy discuss this problem with you > but > now I am starting everything fresh I have completed upto concatanation of > protein with lipid bilayer after that for packing of lipid around protein I > am using inflategro script from teleman website . Problem came in second > step of inflategro i.e for energy minimisation for this I need topology > file > of "protein-lipid system". > I am giving you information in detail i.e - > for topology file I have made changes in topol.top file which I got from > pdb2gmx command in first step for protein processing ,the topol .top file > is > like this- > File 'topol.top' was generated > ; By user: nitu (504) > ; On host: localhost.localdomain > ; At date: Thu Apr 16 23:20:48 2009 > ; > ; This is your topology file > ; Grunge ROck MAChoS > ; > ; Include forcefield parameters > #include "ffG53a6.itp" > > ; Include chain topologies > #include "topol_A.itp" > #include "topol_B.itp" > > ; Include water topology > #include "spc.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > ; Include generic topology for ions > #include "ions.itp" > > [ system ] > ; Name > Grunge ROck MAChoS > > [ molecules ] > ; Compound #mols > Protein_A 1 > Protein_B 1 > ********** > And the change topology file is like this- > > ; Include forcefield parameters > #include "ffG53a6_lipid.itp" > > ; Include chain topologies > #include "topol_A.itp" > #include "topol_B.itp" > > #ifdef POSRES > #include "posre_A.itp" > #include "posre_B.itp" > #endif > > ; Include DMPC chain topology > #include "dmpc.itp" > > > [ system ] > ; Name > Protein in DMPC bilayer > > [ molecules ] > ; Compound #mols > Protein_A 1 > Protein_B 1 > DMPC 128 > > but when I gave this topology file to grompp it shws error- > no. of coordinates in coordinate file doesn,t mach the topology file . > > Can you suggest me something for making topology file for protein-lipid > bilayer system. Is there any other method for making topology file ,I have > read in mannual chapter 5 but there is also mentioned same method. > If possible please help me becoz without solving this problem I can't move > for furthur processing . > > * My gro file of protein shows 9902 atoms . > As you ask in previous mail is .itp file have [ molecules ] section the > answer is the .itp file haven't molecules section it have [molecule type ] > section can it also create problem for topology file working. > > Thanks a lot justin . > I am waiting for your reply. > > Nitu sharma > School of life sciences > Jawaherlal Nehru University > New delhi , India > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090423/45256e1c/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Thu, 23 Apr 2009 10:53:13 +0530 > From: " Y. U. Sasidhar " <[email protected]> > Subject: [gmx-users] validating gromacs installation 4.0.4 > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Users, I posted the following message a few days ago; So far I have > not got any response. Searching archives also seem to indicate that > people are facing similar problems. Some times modifying mdp options > make the tests "pass" as we also observed ( see below ). > > Further the reference trajectories seem to be generated by versions > 3.2/3.3. > > Are there reference trajectories for 4.0.4? > > If some of the tests "fail", does it mean gromacs is not computing as it > should? the results can not be relied on? > > As of now numbers are compared to test pass/failure. > > Can physical properties - like rdf of spc water, diffusion constants > etc- be used to test gromacs? > > I thank you very much for your time. > > The "failures" are presenting a dilemma. I hope I have done what I can > as a user and hope to resolve the issue with your help. > > regards, > > Sasidhar > > PS: we notice that with double precision failures are less; further with > version 3.2 the failures are less suggesting that numerical accuracies > of machines, differences in algorithms, if any, used in different > versions could be a cause for "failures" > ==============previously posted message============= > > > > Dear users, > > We have installed gmx 4.0.4 ( single precision, on cent os 4.3 ( 32 bit > ) on quad core dual xeon machine ( clock 2 GHz ) > > Installation directions as given on the site followed. > And the tests are run using the perl script provided plus test > files/folders. > > We find many failures ( see below ); However, by changing mdp options > all the tests "passed" as detailed below. For example, for the "field" > test coulomb type changed to PME and the test passes with this change. > > The implication is that reference trajectory computed using cut-off > "matches" with newly calculated trajectory using more accurate PME > method. You can see more details below. **So did the tests really pass?** > > We understand energies, virials and forces are compared for all tests to > report errors/failures. > > > When we searched archives we did not find clear solutions to > test-failure-problems. Wiki site does not give any further guidance. > We have looked at wiki site. > > In the presence of failures it is not clear how to proceed further. > > Kindly guide us in upgrading to gmx 4.04 and "clearing" the tests. > regards, > Sasidhar > > > > > > ========================================================================== > This is the output (before making any changes), when i get when i run the > test script gmxtest.pl for 4.0.4 on gromacs-4.0.4. > > $ ./gmxtest.pl all > All 16 simple tests PASSED > FAILED. Check files in field > FAILED. Check files in tip4p > FAILED. Check files in tip4pflex > FAILED. Check files in water > 4 out of 14 complex tests FAILED > FAILED. Check files in kernel020 > FAILED. Check files in kernel120 > FAILED. Check files in kernel121 > FAILED. Check files in kernel122 > FAILED. Check files in kernel123 > FAILED. Check files in kernel124 > FAILED. Check files in kernel220 > FAILED. Check files in kernel221 > FAILED. Check files in kernel222 > FAILED. Check files in kernel223 > FAILED. Check files in kernel224 > FAILED. Check files in kernel320 > FAILED. Check files in kernel321 > FAILED. Check files in kernel322 > FAILED. Check files in kernel323 > FAILED. Check files in kernel324 > 16 out of 63 kernel tests FAILED > N Reference This test > 10 -33.9883 -29.4637 > 11 -33.9883 -29.4637 > There were 2 differences in final energy with the reference file > All 45 pdb2gmx tests PASSED > pdb2gmx tests FAILED > > > The tests which failed previously, passed when following changes were made > to the grompp.mdp files of the failed test directories. > > 1) field : coulombtype : cut-off to PME > 2) tip4p : tempcoupl : berendsen to V-rescale > 3) tip4pflex : vdwtype : cut-off to shift > 4) water : tempcoupl : yes to V-rescale > > 5)kernel020-124 : coulombtype : cut-off to PME & making rlist = rcoulomb > 6)kernel220-224 : coulombtype : recation-field-nec to PME & making rlist = > rcoulomb > > 7)kernel320-324 : coulombtype : switch to PME & making rlist = rcoulomb. > > > > > > > > ------------------------------ > > Message: 5 > Date: Thu, 23 Apr 2009 16:24:39 +1000 > From: Mark Abraham <[email protected]> > Subject: Re: [gmx-users] problem in topology file of protein-lipid > bilayer system for grompp > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > nitu sharma wrote: > > Dear Justin > > > > I am doing simulation of membrane protein .I > > follow your tutorial for that I think its perfect for that. But I am > > getting problem in doing inflategro step, I alredy discuss this problem > > with you but now I am starting everything fresh I have completed upto > > concatanation of protein with lipid bilayer after that for packing of > > lipid around protein I am using inflategro script from teleman website > > . Problem came in second step of inflategro i.e for energy minimisation > > for this I need topology file of "protein-lipid system". > > I am giving you information in detail i.e - > > for topology file I have made changes in topol.top file which I got from > > pdb2gmx command in first step for protein processing ,the topol .top > > file is like this- > > File 'topol.top' was generated > > ; By user: nitu (504) > > ; On host: localhost.localdomain > > ; At date: Thu Apr 16 23:20:48 2009 > > ; > > ; This is your topology file > > ; Grunge ROck MAChoS > > ; > > ; Include forcefield parameters > > #include "ffG53a6.itp" > > > > ; Include chain topologies > > #include "topol_A.itp" > > #include "topol_B.itp" > > > > ; Include water topology > > #include "spc.itp" > > > > #ifdef POSRES_WATER > > ; Position restraint for each water oxygen > > [ position_restraints ] > > ; i funct fcx fcy fcz > > 1 1 1000 1000 1000 > > #endif > > > > ; Include generic topology for ions > > #include "ions.itp" > > > > [ system ] > > ; Name > > Grunge ROck MAChoS > > > > [ molecules ] > > ; Compound #mols > > Protein_A 1 > > Protein_B 1 > > ********** > > And the change topology file is like this- > > > > ; Include forcefield parameters > > #include "ffG53a6_lipid.itp" > > > > ; Include chain topologies > > #include "topol_A.itp" > > #include "topol_B.itp" > > > > #ifdef POSRES > > #include "posre_A.itp" > > #include "posre_B.itp" > > #endif > > I think you've been told before that this is garbage. > [position_restraints] directives are components of a [moleculetype], and > so must come before the [moleculetype] of a subsequent molecule. Your > use of the last four #include preprocessing commands violates this. You > should make two #ifdef POSRES sections appropriately. > > > ; Include DMPC chain topology > > #include "dmpc.itp" > > > > > > [ system ] > > ; Name > > Protein in DMPC bilayer > > > > [ molecules ] > > ; Compound #mols > > Protein_A 1 > > Protein_B 1 > > DMPC 128 > > > > but when I gave this topology file to grompp it shws error- > > no. of coordinates in coordinate file doesn,t mach the topology file . > > OK, so do the arithmetic and see what the problem is. > > > Can you suggest me something for making topology file for protein-lipid > > bilayer system. Is there any other method for making topology file ,I > > have read in mannual chapter 5 but there is also mentioned same method. > > If possible please help me becoz without solving this problem I can't > > move for furthur processing . > > > > * My gro file of protein shows 9902 atoms . > > As you ask in previous mail is .itp file have [ molecules ] section the > > answer is the .itp file haven't molecules section it have [molecule type > > ] section can it also create problem for topology file working. > > So you have 9902 atoms in your coordinate file. How many atoms are in > protein A, protein B and the 128 copies of DMPC *according to their > [moleculetype] definitions*? > > Mark Dear Mark Thanks for your reply. as u ask- how many atoms is------Protein A- 5244 protein B- 4658 And in one dmpc molecule there is 46 atoms so in 128 it is 5888 atoms > can u suggest me how it is helpful in making correct topology file. As you wrote in your mail you should make two # ifdef POSRES section does it means separatly before addind .itp file of Protein A and Protein B???????? > > _______________________________________________ > gmx-users mailing list > [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 60, Issue 116 > ****************************************** >
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