[gmx-users]Simulated annealing

Dear GROMACS users, I have got a problem while running a simulated anealing simulations, using GROMACS 3.3.3 version, of pure water: the task: I want to cool the system (water- 500 molecules) from 360 K to 0K in 100ps time ( fast cooling). For that I used the following script: title

[gmx-users] Fw: Normal mode analysis

How can I obtain normal frequencies and normal modes? How are normal frequencies and normal modes connected with eigenvalues and eigenvectors? Calculation of the system of 3000 atoms with g_nmeig gives 3000 eigenvectors which consists of 3000 coords instead of 9000*9000, why? _

[gmx-users] Fw: Amber to OPLS

Is there any tool to create OPLS topology or obtain charges or is there any library of such topologies (compound of interest: BCL (bacteriochlorophyll) and lycopene? Can I use charges from Amber in OPLS? Thanks in advance. ___ gmx-users mailing list

Re: [gmx-users] mdrun doesn't run in version 4.0 on sgi server

Lee Soin wrote: By invoking "uname -a": Linux sgi4700 2.6.16.46-0.12-default #1 SMP Thu May 17 14:00:09 UTC 2007 ia64 ia64 ia64 GNU/Linux I don't know any other command to retrieve system information. Hmm, that looks like an SGI Altix 4700. IA64 kernels work on those machines. There have be

Re: [gmx-users] mdrun doesn't run in version 4.0 on sgi server

By invoking "uname -a": Linux sgi4700 2.6.16.46-0.12-default #1 SMP Thu May 17 14:00:09 UTC 2007 ia64 ia64 ia64 GNU/Linux I don't know any other command to retrieve system information. 2008/10/27 Mark Abraham <[EMAIL PROTECTED]> > Lee Soin wrote: > >> Everything works fine by setting NOASSEMBLYL

RE: [gmx-users] Fatal error: Invalid dihedral type 0

Hi Mark, I have tried a lot but it still did not work. I just ran a similar case whose file content is similar to what I have right now and it worked , while this always failed. I will post what I have to you. Thank you for your help. Yang From: [E

Re: [gmx-users] mdrun doesn't run in version 4.0 on sgi server

Lee Soin wrote: Everything works fine by setting NOASSEMBLYLOOPS. Thanks! OK. These loops mean GROMACS will run much slower than if one of the optimized sets is used. Please post some fine details of the processor and hardware so there's a chance of working out how to avoid this problem for

Re: [gmx-users] tcoupling

Hi, I haven't really checked how it is with the new version (and you're not telling which version you're using anyway), but grompp used to get confused with multiple molecules and only report the charge on one of them. You can check the total charge from the .tpr file with (bash command line): gm

Re: [gmx-users] tcoupling

shahrbanoo karbalaee wrote: Dear justin ok.you areright.if I add another cl- ,it will negative than more.I know my peptide of charge is +1.please tell me no problem if with warning continue. I'm not clear which warning you're referring to. If you're being told you have a non-zero charge,

[gmx-users] tcoupling

Dear justin ok.you areright.if I add another cl- ,it will negative than more.I know my peptide of charge is +1.please tell me no problem if with warning continue. --best sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs

Re: [gmx-users] tcoupling error

shahrbanoo karbalaee wrote: Dear thanks for your answer. I did as you tell me about usingcapital letter .about charge I guess it related to tfe and protonated amino acid.after change it I still have this warning. Then it's not case sensitivity, but what Mark told you is still

Re: [gmx-users] Pr reach and not reach to equilibria

On Sun, 26 Oct 2008 17:12:26 +0330 "hazizian" <[EMAIL PROTECTED]> wrote: Hi gromacs users I have done Position restrain for 50 ps. after it had finished, I checked the rmsd for confident that rms reached to it's equilibrate mode. When I check it by g_rms command and select system subgroup, I

Re: [gmx-users] mdrun doesn't run in version 4.0 on sgi server

Everything works fine by setting NOASSEMBLYLOOPS. Thanks! 2008/10/26 Mark Abraham <[EMAIL PROTECTED]> > Lee Soin wrote: > >> Single CPU run. These are the last lines of the log file: >> > > Configuring nonbonded kernels... >> Testing ia64 CPU family...Unknown Itanium >> You might want to test th

[gmx-users] Pr reach and not reach to equilibria

Hi gromacs users I have done Position restrain for 50 ps. after it had finished, I checked the rmsd for confident that rms reached to it's equilibrate mode. When I check it by g_rms command and select system subgroup, I find that it had not reached to equilibria, but after I check It by p

[gmx-users] tcoupling error

Dear thanks for your answer. I did as you tell me about usingcapital letter .about charge I guess it related to tfe and protonated amino acid.after change it I still have this warning. best -- sh-karbalaee ___ gmx-users mailing listg

Re: [gmx-users] About the example case "A toy peptide in water" and other protein case (CG martini force field )

Hi, It is not the problem of your command line. It is related to how index file is used with grompp. In general, there are pre-defined groups - protein, non-protein, protein-H, etc; and there are user-defined groups. In your case, Protein1 and TOYPEP are both user-defined groups. So did you mi

Re: [gmx-users] tcoupling

Mark Abraham wrote: shahrbanoo karbalaee wrote: hi justin I have a file tfe peptide water,cl .I minimized it and I want to preequilbrate it.when I do the grompp I get 1 warning: calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations Exclu

Re: [gmx-users] mdrun doesn't run in version 4.0 on sgi server

Lee Soin wrote: Single CPU run. These are the last lines of the log file: Configuring nonbonded kernels... Testing ia64 CPU family...Unknown Itanium You might want to test the speed without assembly kernels by setting the NOASSEMBLYLOOPS environment variable. Try that... My guess is that the

Re: [gmx-users] tcoupling

shahrbanoo karbalaee wrote: hi justin I have a file tfe peptide water,cl .I minimized it and I want to preequilbrate it.when I do the grompp I get 1 warning: calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbour

Re: [gmx-users] mdrun doesn't run in version 4.0 on sgi server

Single CPU run. These are the last lines of the log file: PLEASE READ AND CITE THE FOLLOWING REFERENCE U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 --- Thank You

[gmx-users] tcoupling

hi justin I have a file tfe peptide water,cl .I minimized it and I want to preequilbrate it.when I do the grompp I get 1 warning: calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 turning all