> 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: Question regarding genion (Justin A. Lemkul) > 2. Re: change in rename of 1POPC to 1LIG though coordinate and > atom same in 1LIG of 1POPC, during solvation of system > (Justin A. Lemkul) > 3. Re: Scaling/performance on Gromacs 4 (Manu Vajpai) > 4. Atomtype OW_tip4p not found (Amir Abbasi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 06 Jun 2012 06:04:43 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Question regarding genion > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4fcf2b3b.30...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-15; format=flowed > > > > On 6/6/12 5:38 AM, Matthias Ernst wrote: >> Hi, >> >> I have to questions regarding genion. >> >> 1) Is there a possibility to tell genion in advance which group of molecules >> to >> replace by ions (for me, solvent is always the choice so I want to skript it >> but >> I did not find any parameters for this)? >> > > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts > >> 2) I want to neutralize a charged system. Therefore, as I found out, I can >> use >> the -neutral option. But it seems to me that this option does not work if I >> do >> not specify a concentration (system has a charge of -52): >> genion -s system_in_solvent.tpr -o solventions.gro -p topol_water.top >> -neutral >> [snap] >> Reading file system_in_solvent.tpr, VERSION 4.5.4 (single precision) >> Using a coulomb cut-off of 1 nm >> No ions to add and no potential to calculate. >> >> If I use genion {parameters as above} -conc 0.0 it also won't add ions but if >> I >> try e.g. genion {parameters as above} -c 0.0001, it will add 52 NA and 0 CL >> ions >> which corresponds to a neutral system (with -c 0.001, it will add 53 NA and 1 >> CL >> ions, meaning resulting salt concentration is > 0). I use the amber99sb >> forcefield. >> Is this behaviour desired and do I miss the point of the -neutral option not >> working without specifying a concentration? >> > > I have also found that -neutral must always be used in conjunction with -conc. > It would be nice if this were not the case. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 2 > Date: Wed, 06 Jun 2012 06:08:55 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] change in rename of 1POPC to 1LIG though > coordinate and atom same in 1LIG of 1POPC, during solvation of > system > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4fcf2c37.4040...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > On 6/6/12 3:09 AM, Sangita Kachhap wrote: >> >> Hello all >> I have to do MD simulation of membrane protein having docked ligand in POPC >> lipid bilayer. >> I am geeting error during solvation of system: >> Resname of 1POPC in system_shrink1.gro converted into 1LIG >> >> >> I have done following: >> >> GROMACS COMMAND >> >> 1) Generate topol.top using GROMOS96 53A6 parameter set >> pdb2gmx -f 3gd8-mod.pdb -o 3gd8-mod-processed.gro -water spc >> >> >> at prompt select 14 >> >> 2) Download: >> * popc128.pdb - the structure of a 128-lipid POPC bilayer >> * popc.itp - the moleculetype definition for POPC >> * lipid.itp - Berger lipid parameters >> >> from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies >> >> 3) Modify topol.top with: >> #include "gromos53a6.ff/forcefield.itp" >> >> to: >> >> #include "gromos53a6_lipid.ff/forcefield.itp" >> >> >> & >> >> ; Include Position restraint file >> #ifdef POSRES >> #include "posre.itp" >> #endif >> ; Include ligand topology >> #include "ligand-full.itp" >> >> ; Include POPC chain topology >> #include "popc.itp" >> >> ; Include water topology >> #include "gromos53a6_lipid.ff/spc.itp" >> >> and at the end add LIG 1 in [molecules] >> >> 4) cp files >> aminoacids.rtp >> aminoacids.hdb >> aminoacids.c.tdb >> aminoacids.n.tdb >> aminoacids.r2b >> aminoacids.vsd >> ff_dum.itp >> ffnonbonded.itp >> ffbonded.itp >> forcefield.itp >> ions.itp >> spc.itp >> watermodels.dat >> >> from gromacs top to directory named gromos53a6_lipid.ff in working directory. >> Append parameter ([ atomtypes ], [ nonbond_params ], and [ pairtypes ])from >> lipid.itp to ffnonbonded.itp& ffbonded.itp and create a forcefield.doc file >> that contains a description of the force field parameters contain "GROMOS96 >> 53A6 >> force field, extended to include Berger lipid parameters". >> Delete line ";; parameters for lipid-GROMOS interactions." and its subsequent >> line, change HW as H of [ nonbond_params ] >> >> >> 5) Generate .tpr for POPC >> grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr -maxwarn 1 >> (change OW1, HW2, HW3 to OW, HW and HW2 respectively) >> >> >> 6) Remove periodicity >> trjconv -s em.tpr -f popc128a.pdb -o popc128a_whole.gro -pbc mol -ur compact >> (at command prompt select 0) >> >> >> 7) Oriant the protein within the same coordinate as written in end of >> popc128a_whole.gro >> editconf -f 3gd8-mod-processed.gro -o 3gd8-mod-processe_newbox.gro -c -box >> 6.23910 6.17970 6.91950 >> >> >> 8) Pack lipid around protein >> cat 3gd8-mod-processe_newbox.gro popc128a_whole.gro> system.gro >> >> Remove unnecessary lines (the box vectors from the KALP structure, the header >> information from the DPPC structure and update the second line of the >> coordinate file (total number of atoms) accordingly. >> >> 9) Modify topol.top to add positional restrain on protein >> >> ; Include Position restraint file >> #ifdef POSRES >> #include "posre.itp" >> #endif >> >> ; Strong position restraints for InflateGRO >> #ifdef STRONG_POSRES >> #include "strong_posre.itp" >> #endif >> >> ; Include DPPC chain topology >> #include "dppc.itp" >> >> ; Include water topology >> #include "gromos53a6_lipid.ff/spc.itp" >> >> & >> Genrate new positional restraint >> genrestr -f 3gd8-mod-processe_newbox.gro -o strong_posre.itp -fc 100000 >> 100000 >> 100000 >> for system (protein + ligand) >> Add a line "define = -DSTRONG_POSRES" to .mdp file >> >> >> 10) addion POPC 128 to topol.top >> >> >> 11) Scale down lipid >> perl inflategro.pl system.gro 0.95 POPC 0 system_shrink1.gro 5 >> area_shrink1.dat >> >> >> >> 12) Solvate with water >> >> Copy vdwradii.dat from Gromacs top to working directory and change the value >> of >> C from 0.15 to 0.375(to avoid addition of water in lipid hydrohphobic core) >> >> genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro -p >> topol.top >> >> >> Upto 11th step .gro file is OK conatin protein resid 32-254, ligand 1LIG, >> POPC >> resid 1-128 and solvent >> >> After 12th step in gro file protein is there 32-254, Ligand 1LIG but POPC >> resid >> 2-128 because resid 1 of POPC is converted to 1LIG though all cordinate and >> atom >> name are same of 1POPC in 1LIG. >> >> >> >> Anybody please suggest me why this change in rename is occuring. >> > > Based on the description, you say in step (3) that you add "LIG 1" to the end > of > [molecules], but then in (12) you give the order as protein, ligand, then > POPC. > The order of the coordinate file and [molecules] must match, otherwise funny > things happen. If you have protein, ligand, and POPC, you must list the > moleculetype names in that order in [molecules]. >
Thanks for reply In step 3 I added "LIG 1" to the end of [molecules] because when I used command "pdb2gmx -f 3gd8-mod.pdb -o 3gd8-mod-processed.gro -water spc" to generate topol.top it already contain "Protein_chain_A 1" in [molecules] so I added only "LIG 1" This is end of topol.top after solvation [ molecules ] ; Compound #mols Protein_chain_A 1 LIG 1 POPC 128 SOL 1829 > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 3 > Date: Wed, 6 Jun 2012 16:49:08 +0530 > From: Manu Vajpai <manuvaj...@gmail.com> > Subject: Re: [gmx-users] Scaling/performance on Gromacs 4 > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <CAHv4Ge1b-7pMQ5vy+FFrAwY8VY7jYVf4Z9okSnvRUXA2_Um=f...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Apologies for reviving such an old thread. For clarifications, interlagos > and bulldozer both have a modular architecture, as mentioned earlier. Each > bulldozer module has 2 integer cores and one floating point unit shared > between the two cores. So, although you have 64 cores (counting integer > cores) reported by the os, the number of floating point units is still 32. > Moreover, each FP unit can process two threads when it is possible, but > since gromacs is so compute intensive I am guessing it is saturated by just > one. Hence you are not observing a scale-up by moving from 32 to 64 > threads. > > Regards, > Manu Vajpai > IIT Kanpur > > On Fri, Mar 16, 2012 at 4:24 PM, Szil?rd P?ll <szilard.p...@cbr.su.se>wrote: > >> Hi Sara, >> >> The bad performance you are seeing is most probably caused by the >> combination of the new AMD "Interlagos" CPUs, compiler, operating >> system and it is very likely the the old Gromacs version also >> contributes. >> >> In practice these new CPUs don't perform as well as expected, but that >> is partly due to compilers and operating systems not having full >> support for the new architecture. However, based on the quite >> extensive benchmarking I've done, the with such a large system should >> be considerably better than what your numbers show. >> >> This is what you should try: >> - compile Gromacs with gcc 4.6 using the "-march=bdver1" optimization flag; >> - have at least 3.0 or preferably newer Linux kernel; >> - if you're not required to use 4.0.x, use 4.5. >> >> Note that you have to be careful with drawing conclusions from >> benchmarking on small number of cores with large systems; you will get >> artifacts from caching effects. >> >> >> And now a bit of fairly technical explanation, for more details ask Google >> ;) >> >> The machine you are using has AMD Interlagos CPUs based on the >> Bulldozer micro-architecture. This is a new architecture, a departure >> from previous AMD processors and in fact quite different from most >> current CPUs. "Bulldozer cores" are not the traditional physical >> cores. In fact the hardware unit is the "module" which consists of two >> "half cores" (at least when it comes to floating point units). and >> enable a special type of multithreading called "clustered >> multithreading". This is slightly similar to the Intel cores with >> Hyper-Threading. >> >> >> Cheers, >> -- >> Szil?rd >> >> >> >> On Mon, Feb 20, 2012 at 5:12 PM, Sara Campos <srrcam...@gmail.com> wrote: >> > Dear GROMACS users >> > >> > My group has had access to a quad processor, 64 core machine (4 x Opteron >> > 6274 @ 2.2 GHz with 16 cores) >> > and I made some performance tests, using the following specifications: >> > >> > System size: 299787 atoms >> > Number of MD steps: 1500 >> > Electrostatics treatment: PME >> > Gromacs version: 4.0.4 >> > MPI: LAM >> > Command ran: mpirun -ssi rpi tcp C mdrun_mpi ... >> > >> > #CPUS Time (s) Steps/s >> > 64 195.000 7.69 >> > 32 192.000 7.81 >> > 16 275.000 5.45 >> > 8 381.000 3.94 >> > 4 751.000 2.00 >> > 2 1001.000 1.50 >> > 1 2352.000 0.64 >> > >> > The scaling is not good. But the weirdest is the 64 processors performing >> > the same as 32. I see the plots from Dr. Hess on the GROMACS 4 paper on >> JCTC >> > and I do not understand why this is happening. Can anyone help? >> > >> > Thanks in advance, >> > Sara >> > >> > -- >> > 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! >> > 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 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! >> 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 >> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120606/4a86cf4c/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Wed, 6 Jun 2012 04:19:05 -0700 (PDT) > From: Amir Abbasi <amir.abbas...@yahoo.com> > Subject: [gmx-users] Atomtype OW_tip4p not found > To: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > Message-ID: <1338981545.609.yahoomail...@web113012.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi! > I use tleap to generate topology file of a RNA molecule with parmbsc0 ff. > Then I > generate .gro and .top files of that with amb2gmx.pl. > I'm manually add this lines to .top file > > ; Include water topology > #include "amber99sb.ff/tip4p.itp" > > ; Include topology for ions > #include "amber99sb.ff/ions.itp" > ?but after running this code: > > grompp -f ions.mdp -c ribozyme_solv.gro -p ribozyme.top -o ions.tpr > > ?I've got this error message: > > Program grompp, VERSION 4.5.5 > Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line: 1166 > > Fatal error: > Atomtype OW_tip4p not found > > > what should I do? > > Regards, > Amir > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120606/a1430df2/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 98, Issue 35 > ***************************************** > Sangita Kachhap SRF BIC,IMTECH CHANDIGARH ______________________________________________________________________ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202 -- 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! 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