[gmx-users] solvent group size (12548) is not a multiple of 3
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 10 10 10 (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 __ 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 listgmx-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
Re: [gmx-users] poor performance in Hemiltonian Replica Exchange
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 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 -- gmx-users mailing listgmx-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] poor performance in Hemiltonian Replica Exchange
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 listgmx-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
Re: [gmx-users] keep the nanotube cylindrical.
On Sat, May 5, 2012 at 7:27 PM, Za Pour 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 Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing listgmx-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] Re: gmx-users Digest, Vol 97, Issue 69
ns ) To: gmx-users@gromacs.org Message-ID: Content-Type: text/plain; charset=ISO-8859-1 Dear all, I want to calculate the ion solvation free energy (e.g. an ion Na+ solvated in a water box) using Bennett Acceptance Ratio (BAR) method, following the tutorial by Justin A. Lemkul. However, if I turn off the Coulombic interaction, the total charge of my system would not neutral at all. Does this affact my calculation? = Dechang Li , Ph.D Biomechanics and Biomaterials Laboratory Department of Applied Mechanics School of Aerospace Engineering Beijing Institute of Technology Beijing 100081, P. R. China = -- Message: 7 Date: Thu, 10 May 2012 14:59:58 +0530 From: Debayan Chakraborty Subject: [gmx-users] Treating solute as a rigid body with flexible solvent molecules To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset="iso-8859-1" Dear Gromacs Users, I want to simulate an organic dye in a solvent ( such as aniline as DMA). I have already relaxed the solvent around the dye in the equilibration run ( NPT) using position restraints on the solute. Now for the production run I want to release the position restraints on the dye and allow it to translate and rotate like a rigid body under the influence of the solvent. I am new to GROMACS, and I am not sure what is the best way to realise this. Any help would be greatly appreciated. Best Regards, Debayan Chakraborty -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120510/5e86e64b/attachment-0001.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 69 *-- gmx-users mailing listgmx-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
Re: [gmx-users] Free energy calculation about ions (hope Justin A. Lemkul can give some suggestions )
On 5/9/12 10:37 PM, DeChang Li wrote: Dear all, I want to calculate the ion solvation free energy (e.g. an ion Na+ solvated in a water box) using Bennett Acceptance Ratio (BAR) method, following the tutorial by Justin A. Lemkul. However, if I turn off the Coulombic interaction, the total charge of my system would not neutral at all. Does this affact my calculation? I would think so. There have been numerous discussion on this topic over the years, so please consult the mailing list archive. Among the more interesting posts you're likely to find: http://lists.gromacs.org/pipermail/gmx-users/2006-September/023973.html http://lists.gromacs.org/pipermail/gmx-users/2006-March/020677.html http://lists.gromacs.org/pipermail/gmx-users/2008-February/032541.html There is published literature on ion hydration free energies, so do some literature searching to see how others handle such situations. Even a simple Google search turns up some useful information. -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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Treating solute as a rigid body with flexible solvent molecules
On 10/05/2012 7:29 PM, Debayan Chakraborty wrote: Dear Gromacs Users, I want to simulate an organic dye in a solvent ( such as aniline as DMA). I have already relaxed the solvent around the dye in the equilibration run ( NPT) using position restraints on the solute. Now for the production run I want to release the position restraints on the dye and allow it to translate and rotate like a rigid body under the influence of the solvent. I am new to GROMACS, and I am not sure what is the best way to realise this. Any help would be greatly appreciated. This kind of procedure is done in lots of simulations - have a look at some tutorial material and you should learn how to do this, and a lot more besides! Mark -- gmx-users mailing listgmx-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
