> 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: keep the nanotube cylindrical. (Elton Carvalho) > 2. poor performance in Hemiltonian Replica Exchange (francesco oteri) > 3. Re: poor performance in Hemiltonian Replica Exchange > (Michael Shirts) > 4. solvent group size (12548) is not a multiple of 3 > (Sangita Kachhap) > 5. rvdw and DispCorr (Bernhard Knapp) > 6. Re: solvent group size (12548) is not a multiple of 3 (Terry) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 10 May 2012 16:21:31 +0200 > From: Elton Carvalho <elto...@if.usp.br> > Subject: Re: [gmx-users] keep the nanotube cylindrical. > To: Za Pour <za.p...@yahoo.com>, Discussion list for GROMACS users > <gmx-users@gromacs.org> > Message-ID: > <caoyvbokmjs-te_r-6uxh+k8zmct83mmknjnuccazfzd+wpp...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Sat, May 5, 2012 at 7:27 PM, Za Pour <za.p...@yahoo.com> wrote: >> Dear gmx users >> I am simulation a system including carbon nanotube+water.I have done these >> things: >> However as I looked into the nvt.gro I realized that the cylindrical shape >> of carbon nanotube >> ?has been changed.I am not sure what I have done is correct or not?and how >> to keep nanotube cylindrical ? any help would be really appreciated. >> ????? Best regards > > I had a similar issue, but I modeled the CNT carbon atoms as opls_147, > trying not to change the parameters too much, so I kept the bond > lengths, angles and force constants untouched. > > I noticed that removing the [ dihedrals ] section from the resulting > topology significantly reduced the tube deformation. Since g_x2top > doesn't generate impropers and a CNT has no rotable bonds, these > dihedrals are spurious, anyway. > > Also, do your tubes have open ends? If you can afford to have periodic > tubes, so that the box z length is a multiple of the tube unit cell > and the tube ends are bonded through the box wall, it seems much more > stable. > Or you could try capped tubes. > > > -- > Elton Carvalho > Tel.: +55 11 3091-6985/6922 > Dept F?sica dos Materiais e Mec?nica > Instituto de F?sica > Universidade de S?o Paulo > P.O. Box 66318 - 05314-970 S?o Paulo-SP, Brazil > > > ------------------------------ > > Message: 2 > Date: Thu, 10 May 2012 18:23:54 +0200 > From: francesco oteri <francesco.ot...@gmail.com> > Subject: [gmx-users] poor performance in Hemiltonian Replica Exchange > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <CAFQcp-PpW0prmq=uuMCAJcOoEgQYwbP1=berej-insh_af4...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear gromacs users, > > I performed a Hemiltonian Replica Exchange (i.e. replica exchange where > each replica has a init_lambda=0, delta_lambda=0 and init_lambda ranging > uniformely from 0 to 1). > > Since I have only ten fixed discrete lambda, I run a Temperature Replica > Exchange where, for each replica I generated a .top file with the parameter > rescaled through a > python script ( in practice I did through python the same thing gromacs is > supposed to do with the H-REM previously described). Now gromacs complained > because > every replica has the same setup, so I changed the temperatures using very > close values (300.0001K, > 300.0002K,300.0003K,300.0004K,300.0005K,300.0006K,300.0007K,300.0008K, > 300.0009K) > With this setup the simulation runs fine and I expect to have similar > result. > > Then I compared the results observing two phenomena: > > 1) In the second case exchange rate is 100%, while in the first case I have > an exchange rate close to 30%. > Does it rise because the temperatures are too close? > > 2) The second setup is 3x faster! > In particular I observe an imbalance between PME and force calculation > ranging from 10% to 60%. > I tried to run each replia indipendently (a different mdrun instance for > each .tpr file) but still I observe the same performance slowdown. > I guess the free energy impairs the efficient force calculation, but I dont > understand why. > > Can someone explain me the two observations? > > > > Francesco > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120510/f5452d69/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Thu, 10 May 2012 14:20:44 -0400 > From: Michael Shirts <mrshi...@gmail.com> > Subject: Re: [gmx-users] poor performance in Hemiltonian Replica > Exchange > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <CA+zJb=g8dzPf137+uOaWhEsi57FmFW8DJF6aw--wbi3v=ow...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > 4.6 will include Hamiltonian replia exchange functionality built into > the MPI version. > > Currently the description of the error is very vague -- if you can > write up what exactly the numbers are, and what they should be, with > files that exactly replicate the error, then I can take a look. But > unless I can reproduce the error you are describing out of the box, > its unlikely I will be able to find it. > > Additionally, it would be easiest if the files were deposited as a > redmine bug report, so that the information is centrally located. > > Best, > Michael > > On Thu, May 10, 2012 at 12:23 PM, francesco oteri > <francesco.ot...@gmail.com> wrote: >> Dear gromacs users, >> >> I performed a Hemiltonian Replica Exchange (i.e. replica exchange where each >> replica has a init_lambda=0,?delta_lambda=0 and?init_lambda ranging >> uniformely from 0 to 1). >> >> Since I have only ten fixed discrete?lambda, I run a Temperature Replica >> Exchange where, for each replica I generated a .top file with the parameter >> rescaled through a >> python script ( in practice I did through python the same thing gromacs is >> supposed to do with the H-REM previously described). Now gromacs complained >> because >> every replica has the same setup, so I changed the temperatures using very >> close values (300.0001K, >> ?300.0002K,300.0003K,300.0004K,300.0005K,300.0006K,300.0007K,300.0008K,?300.0009K) >> With this setup the simulation runs fine and I expect to have similar >> result. >> >> Then I compared the results observing two phenomena: >> >> 1) In the second case exchange rate is 100%, while in the first case I have >> an exchange rate close to 30%. >> Does it rise ?because the temperatures are too close? >> >> 2) The second setup is 3x faster! >> In particular I observe an imbalance between PME and force calculation >> ranging from 10% to 60%. >> I tried to run each replia indipendently (a different mdrun instance for >> each .tpr file)?but still I observe the same performance slowdown. >> I guess the free energy impairs the efficient force calculation, but I dont >> understand why. >> >> Can someone explain me the two observations? >> >> >> >> Francesco >> >> -- >> 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 > > > ------------------------------ > > Message: 4 > Date: Fri, 11 May 2012 11:48:26 +0530 (IST) > From: "Sangita Kachhap" <sang...@imtech.res.in> > Subject: [gmx-users] solvent group size (12548) is not a multiple of 3 > To: gmx-users@gromacs.org > Message-ID: > <43695.172.141.121.99.1336717106.squir...@webmail.imtech.res.in> > Content-Type: text/plain;charset=utf-8 > > > Hello all > I am runing Gromacs Tutorial KALP-15 in DPPC (I am using POPC) > I am geeting error during addiotion of ions > Fatal error: > Your solvent group size (12548) is not a multiple of 3 > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > I have done following: > > GROMACS COMMAND > > 1) Generate topol.top using GROMOS96 53A6 parameter set > pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc > > ay prompt select 13, 2, 2 > > 2) Download: > * dppc128.pdb - the structure of a 128-lipid DPPC bilayer > * dppc.itp - the moleculetype definition for DPPC > * 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 POPC chain topology > #include "popc.itp" > > ; Include water topology > #include "gromos53a6_lipid.ff/spc.itp" > > > > 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 KALP peptide within the same coordinate as written in end of > popc128a_whole.gro > editconf -f KALP-15_processed.gro -o KALP_newbox.gro -c -box 6.23910 6.17970 > 6.91950 > > > 8) Pack lipid around protein > cat KALP_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 KALP_newbox.gro -o strong_posre.itp -fc 100000 100000 100000 > (at prompt select 2) > > Add a line "define = -DSTRONG_POSRES" to .mdp file > > > > > 10) Scale down lipid > perl inflategro.pl system.gro 0.95 POPC 0 system_shrink1.gro 5 > area_shrink1.dat > system_shrink1.gro > > > 11) addion POPC 128 to topol.top > > > 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 > > > grompp -f ions.mdp -c system_shrink1_solv.gro -p topol.top -o ions.tpr > > genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname CL > -nn > 4 > (at command prompt select 0) > > > > So can anyone please help me correct this error. > > > > With regards > Sangita Kachhap > SRF > BIC,IMTECH > CHANDIGARH > > ______________________________________________________________________ > ??????????????????????????�??? ???????????????????????????????????� > ????????????????????? (??????????????????????????? ???????????????????????? > ???????????????????????? ???????????????) > Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) > ?????????????????? 39 ???, ??????????????�????????? / Sector 39-A, Chandigarh > ????????? ?????????/PIN CODE :160036 > ??????????????????/EPABX :0172 6665 201-202 > > > ------------------------------ > > Message: 5 > Date: Fri, 11 May 2012 10:23:50 +0200 > From: Bernhard Knapp <bernhard.kn...@meduniwien.ac.at> > Subject: [gmx-users] rvdw and DispCorr > To: gmx-users@gromacs.org > Message-ID: <4faccc96.8070...@meduniwien.ac.at> > Content-Type: text/plain; charset=ISO-8859-15; format=flowed > > Dear gromacs users > > In a recent paper I found the following protocol of a gromacs simulation: > > "All simulations were performed with the GROMACS 4.0 [12] compiled in > single-precision mode at a constant temperature of 277 K in a periodic box > with > an edge length of approximately 8.2 nm and the default GROMOS-96 43A1 > forcefield > [22]. The simulation systems each contained approximately 16,500 Simple Point > Charge (SPC) water molecules [23]. Short-range interactions were evaluated > using > a neighbor list of 1.0 nm updated at every 10 steps. Van der Waals > interactions > used a cutoff with a smoothing > function such that the interactions slowly decayed to zero between 0.75 nm and > 0.90 nm. A long-range analytical dispersion correction was applied to the > energy > and pressure to account for the truncation of the Lennard-Jones interactions > [24]. Electrostatic interactions were evaluated using the particle mesh Ewald > (PME) [25] with a real space cutoff of 1.0 nm, a spline order of 6, a Fourier > spacing of 0.1 m, and relative tolerance between long and short range energies > of . All bonds to hydrogen > were constrained with LINCS [26] with an order of 12, and a time step of 2 fs > was used for dynamics." > > In the gromacs manual 4.5.4, page 104 it says: "The GROMOS-96 force field was > parameterized with a Lennard-Jones cut-off of 1.4 nm, so be sure to use a > Lennard-Jones cut-off (rvdw) of at least 1.4". > > Is it a good idea to set "DispCorr" to "EnerPres" and reduce the rvdw so > dramatically (almost the half value)? > > And a second question: Is there a study on the percentage of information > getting > lost when reducing the rvdw with and without dispcorr (e.g. to 1.2, 1.0, etc) > if > the forcefield was parameterized with 1.4? > > best, > Bernhard > > > > > > ------------------------------ > > Message: 6 > Date: Fri, 11 May 2012 16:41:16 +0800 > From: Terry <terrence...@gmail.com> > Subject: Re: [gmx-users] solvent group size (12548) is not a multiple > of 3 > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <CAM9kr8haSWn64DZ=ay_wcz_kq34rmhxrwrzkacye1jnbyvl...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Fri, May 11, 2012 at 2:18 PM, Sangita Kachhap <sang...@imtech.res.in>wrote: > >> >> Hello all >> I am runing Gromacs Tutorial KALP-15 in DPPC (I am using POPC) >> I am geeting error during addiotion of ions >> Fatal error: >> Your solvent group size (12548) is not a multiple of 3 >> For more information and tips for troubleshooting, please check the GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> ------------------------------------------------------- >> >> I have done following: >> >> GROMACS COMMAND >> >> 1) Generate topol.top using GROMOS96 53A6 parameter set >> pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc >> >> ay prompt select 13, 2, 2 >> >> 2) Download: >> * dppc128.pdb - the structure of a 128-lipid DPPC bilayer >> * dppc.itp - the moleculetype definition for DPPC >> * 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 POPC chain topology >> #include "popc.itp" >> >> ; Include water topology >> #include "gromos53a6_lipid.ff/spc.itp" >> >> >> >> 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 KALP peptide within the same coordinate as written in end of >> popc128a_whole.gro >> editconf -f KALP-15_processed.gro -o KALP_newbox.gro -c -box 6.23910 >> 6.17970 >> 6.91950 >> >> >> 8) Pack lipid around protein >> cat KALP_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 KALP_newbox.gro -o strong_posre.itp -fc 100000 100000 100000 >> (at prompt select 2) >> >> Add a line "define = -DSTRONG_POSRES" to .mdp file >> >> >> >> >> 10) Scale down lipid >> perl inflategro.pl system.gro 0.95 POPC 0 system_shrink1.gro 5 >> area_shrink1.dat >> system_shrink1.gro >> >> >> 11) addion POPC 128 to topol.top >> >> >> 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 >> >> >> grompp -f ions.mdp -c system_shrink1_solv.gro -p topol.top -o ions.tpr >> >> genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname >> CL -nn 4 >> (at command prompt select 0) >> > > Is group 0 your solvent? You should chose a group corresponding to the > solvent of your system.
Thans for reply. I got it its 15 not 0, now its working fine. > > > >> >> >> >> So can anyone please help me correct this error. >> >> >> >> With regards >> Sangita Kachhap >> SRF >> BIC,IMTECH >> CHANDIGARH >> >> ______________________________________________________________________ >> ??????????????????????????�??? ???????????????????????????????????� >> ????????????????????? (??????????????????????????? ???????????????????????? >> ???????????????????????? ???????????????) >> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) >> ?????????????????? 39 ???, ??????????????�????????? / Sector 39-A, Chandigarh >> ????????? ?????????/PIN CODE :160036 >> ??????????????????/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! >> 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/20120511/098f86c1/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 97, Issue 71 > ***************************************** > 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! 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