[gmx-users] R: Tabulated potentials
I forgot to add that I start from a liquid system and that my simulation is run in microcanonical system at a temperature well below the melting point for argon. Francesco Mambretti Il 03/11/14 11:57, Francesco Mambretti francesco.mambre...@studenti.unimi.it ha scritto: Dear GROMACS users and developers, I am using GROMACS 5.0.1. I would like to use tabulated potentials (Aziz ones for argon and krypton in particular); as a starting test, I began with LJ tabulated potential. I followed the instructions on the manual, and I did well because my .xvg file of Lennard-Jones 6-12 was substantially identical to the one provided in /share/gromacs/top/table6-12.xvg. I set the .top file and .mdp file according to the instructions on the website and on the manual, besides following the attached pdf in http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated. .top [ defaults ] section has nbfunc and comb-rule equal to 1; C and A parameters in the [ atomtypes ] sections are set equal to 4 epsilon sigma^6 and 4 epsilon sigma^12 respectively. .mdp parameters are: cutoff-scheme = group, coulombtype = user and vdwtype = user. My system is a molecular system of 256 argon atoms. PBC = xyz, no long-range dispersion corrections. Until now, all worked fine. The problems began when I decided to freeze a group of atoms in my system. I added the right atom numbers to the index file, and add energy group exclusions in the .mdp file. Moreover, I specified in the .mdp that I wanted the motion frozen in the 3 directions. The problem is that ordinary LJ of GROMACS (not tabulated) goes on well, and the system solidifies around the frozen seed (an fcc-like seed of 13 atoms); but, with the same conditions, LJ tabulated (also with the table given in the share/top folder) behaves differently. In particular, frozen atoms seem to repulse very strongly the others, in such a way that a hole creates around the frozen nucleus. Also the g(r) are very different, and while in the first case I obtain a more or less ordered solid, in the latter I obtain a strongly disordered solid. What am I missing? Should I apply particular switches or corrections? Why does GROMACS behaves differently if I give it the same potential, but tabulated in the latter case and not tabulated in the first? The only thing that changed between the two cases is the use of a tabulated interaction instead that LJ GROMACS default. Do you know anything about similar problems with freeze groups? Thanks a lot Francesco Mambretti -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Tabulated potentials
Dear GROMACS users and developers, I am using GROMACS 5.0.1. I would like to use tabulated potentials (Aziz ones for argon and krypton in particular); as a starting test, I began with LJ tabulated potential. I followed the instructions on the manual, and I did well because my .xvg file of Lennard-Jones 6-12 was substantially identical to the one provided in /share/gromacs/top/table6-12.xvg. I set the .top file and .mdp file according to the instructions on the website and on the manual, besides following the attached pdf in http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated. .top [ defaults ] section has nbfunc and comb-rule equal to 1; C and A parameters in the [ atomtypes ] sections are set equal to 4 epsilon sigma^6 and 4 epsilon sigma^12 respectively. .mdp parameters are: cutoff-scheme = group, coulombtype = user and vdwtype = user. My system is a molecular system of 256 argon atoms. PBC = xyz, no long-range dispersion corrections. Until now, all worked fine. The problems began when I decided to freeze a group of atoms in my system. I added the right atom numbers to the index file, and add energy group exclusions in the .mdp file. Moreover, I specified in the .mdp that I wanted the motion frozen in the 3 directions. The problem is that ordinary LJ of GROMACS (not tabulated) goes on well, and the system solidifies around the frozen seed (an fcc-like seed of 13 atoms); but, with the same conditions, LJ tabulated (also with the table given in the share/top folder) behaves differently. In particular, frozen atoms seem to repulse very strongly the others, in such a way that a hole creates around the frozen nucleus. Also the g(r) are very different, and while in the first case I obtain a more or less ordered solid, in the latter I obtain a strongly disordered solid. What am I missing? Should I apply particular switches or corrections? Why does GROMACS behaves differently if I give it the same potential, but tabulated in the latter case and not tabulated in the first? The only thing that changed between the two cases is the use of a tabulated interaction instead that LJ GROMACS default. Do you know anything about similar problems with freeze groups? Thanks a lot Francesco Mambretti -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Cardiolipin all-atom PDB and parameters (.itp)
Hello gmx-users, I am looking for Cardiolipin's PDB and parameter (.itp) file. (Cardiolipin: an important component of the inner mitochondrial membrane) I looked through the user's list but could not find anything (some links have been specified which are now inactive) Could anyone please suggest. Thanks, sxn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to overcome the error Atom P in residue DC 3 was not found in the rtp entry DC5 with 28 atoms while sorting atom.
On 11/3/14 12:32 AM, Seera Suryanarayana wrote: Dear gromacs users I have been tried to simulate the protein-dna complex. I got error as Atom P in residue DC 3 was not found in the rtp entry DC5 with 28 atoms while sorting atom upon using the command pdb2gmx. I have been added the P atom and bonds of P in the .rtp file which is the part of AMBER99SB-ILDN force field. After the modification of the dna.rtp file I also got the same error which mentioned above. Kindly tell me how to overcome this error. DNA does not normally have a 5'-PO4 cap, but apparently your structure does. If it's some biologically interesting state, you'll need to add a .tdb entry to deal with having a phosphate group. If not, delete the extraneous atoms. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] size of the box for peptide
Dear gromacs users, I want to simulate the conformation of peptide in solution (20 monomers of Glutamate with solution). I am in doubt about the size of the box, and number of water molecules. I want to consider rhombic dodecahedron box. For example I chose a box with approximately 498 nm^3 that contain 16369 water molecules. I did NVT and NPT equilbiration and I checked the density and it is fine. My question is that how I can chose the smallest cell that also no interaction between peptides form neighbouring PBC cell. As I want to use BP-REMD simulations, it is important to have the efficient size of the system without any interaction between polymers. Thanks very much, Leila -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulating Multiple Solute Particles
On 11/3/14 12:50 AM, Nathan K Houtz wrote: Sorry everybody, I accidentally unsubscribed from the mailing list and missed my last response. Dr. Lemkul posted a message but I can't reply directly to it, so here's what he said: Your topology is constructed incorrectly, but without seeing it in its entirety, it is impossible to say. Please post the file for download somewhere and provide a link, otherwise copy and paste its entire contents into a reply if the message will be small enough. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul Thank you Justin! I think it's easier to just paste it here. This is my topol.top file: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.5 [ atomtypes ] ;name at.num mass charge ptype sigma epsilon CH3 15 15.035000.000 A 0.39100 0.66944 ;united atom Methyl [C-CH3] C 12 12.011000.000 A 0.35000 0.27614 ;C [R3CCOO-] (first carbon) CM 12 12.011000.000 A 0.37500 0.43932 ;carboxyl C [R-(C=O)-OH] O8 15.999400.000 A 0.30800 0.71128 ;carboxyl O [C-O-H] OM8 15.999400.000 A 0.29600 0.87864 ;carbonyl O [C=O] H11.007940.000 A 0.0 0.0 ;carboxyl H [C-O-H] OW8 15.999400.000 A 0.31660 0.65000 HW11.007940.000 A 0.0 0.0 [ moleculetype ] ; Namenrexcl TETR3 [ atoms ] ; nrtype resnr residuatomcgnr charge mass 1 CH3 1TETR C1 1 0 15.03500 2 C 1TETR C2 1 0 12.01100 3 C 1TETR C3 1 0 12.01100 4 CM 1TETR C4 1 0.38 12.01100 5 OM 1TETR O1 1 -0.38 15.99940 6 O 1TETR O2 1 -0.40 15.99940 7 H 1TETR H4 1 0.401.00794 [constraints] ; i j funct distance 1 2 10.14550 2 3 10.11780 3 4 10.14420 4 5 10.12040 4 6 10.13100 6 7 10.89000 ; Include SPC water topology #include oplsaa.ff/tip3p.itp Here's your problem. Look at the contents of tip3p.itp: [ atoms ] ; idat type res nr residu name at name cg nr charge 1 opls_111 1 SOL OW 1 -0.834 2 opls_112 1 SOL HW1 10.417 3 opls_112 1 SOL HW2 10.417 It uses OPLS-AA atom types, but you haven't defined what those are because nothing above calls the OPLS-AA force field. Hence, grompp dies because it does not know how to assign nonbonded parameters to opls_111 or opls_112. [ system ] Tetrolic Acid in water [ molecules ] Tetrolic Acid 500 SOL 5481 I made the file myself, so I hope I didn't make any syntax errors. I discovered with the .gro file that the spacing is very important since gromacs doesn't use delimiters but allows only a fixed number of characters for each entry. Is the .top file the same way? I just used a template from some example file and tried to make the numbers fit appropriately under the headings. If it's not correct, why didn't gromacs complain when I solvated it? Doesn't it read in the topology file then as well? Topologies do not have the same formatting requirements. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization of an UNKNOWN molecule.
On 11/3/14 12:57 AM, Kalyanashis Jana wrote: Thank you very much... But I am not going to use any parent molecules like protein or DNA. I would like to perform the gromacs simulation for this unknown molecule. First few lines of my topology file.. ; ; File 'topol.top' was generated ; By user: kollan (506) ; On host: master.localdomain ; At date: Sun Nov 2 20:28:10 2014 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.6.3 ; ; Command line was: ; pdb2gmx -f A-T.pdb -o A-T1.pdb -p topol.top ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters # include A-T.itp ; ; Built itp for A-T.mol2 ;by user vzoete Mon Oct 27 06:32:46 CET 2014 ; ; [ atomtypes ] The yellow colored lines are first seven line A-T.itp file And the error was Fatal error: Syntax error - File A-T.itp, line 7 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Please help me.. You'll need to show us what is in A-T.itp, because that's where the problem is. Probably you're missing a [defaults] directive, but that's just a guess. -Justin On Mon, Nov 3, 2014 at 1:28 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/14 11:32 AM, Kalyanashis Jana wrote: Thank you so much... I have tried to run the grompp step according to you. But it is showing Fatal error: Syntax error - File A-T.itp, line 7 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes I have attached the .itp file and .top file. Please kindly tell me, what to do now.. Force-field level directives must be declared before molecule-level directives. So if your ligand requires new bonded or nonbonded parameters, or new atom types, it must be #included before the declaration of any [moleculetype]. So put your #include statement for the ligand topology immediately after the #include statement for the parent force field. -Justin On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia rosas.vic...@gmail.com wrote: just put the itp file in your working directory, and include it in the top file of your system, so that Gromacs can find it. Hope this helps. Victor 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com: Dear all, I am trying to run a gromacs simulation using an .itp file of an unknown molecule ( non protein and DNA). I don't want to put the .itp file in a forcefield folder and I would like put it in my working directory. Can you please tell me, what is procedure to finish the energy minimization? Please help me.. Thanks in advance, Kalyanashis -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Cardiolipin all-atom PDB and parameters (.itp)
On 11/3/14 12:22 PM, shivangi nangia wrote: Hello gmx-users, I am looking for Cardiolipin's PDB and parameter (.itp) file. (Cardiolipin: an important component of the inner mitochondrial membrane) I looked through the user's list but could not find anything (some links have been specified which are now inactive) Note that the archive still exists fully, and you can use the date within the URL to access the right page. As to the cardiolipin issue, try CHARMM-GUI. There are dozens of lipids available there as part of the membrane builder. Otherwise, find a reliable paper that has done simulations and ask the corresponding author to share the topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Cardiolipin all-atom PDB and parameters (.itp)
Hi Shivangi, Do you have a specific cardiolipin in mind? Cheers, Tsjerk On Nov 3, 2014 6:23 PM, shivangi nangia shivangi.nan...@gmail.com wrote: Hello gmx-users, I am looking for Cardiolipin's PDB and parameter (.itp) file. (Cardiolipin: an important component of the inner mitochondrial membrane) I looked through the user's list but could not find anything (some links have been specified which are now inactive) Could anyone please suggest. Thanks, sxn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Postdoctoral Position at U.S. Army Research Laboratory in Coarse-Grain Modeling and Simulation
A postdoctoral position is available immediately at the U.S. Army Research Laboratory. The position involves the continued development of bottom-up coarse-grain methodologies built around the molecular dynamics and dissipative particle dynamics methods. The project is part of a multiscale experimental and computational research program, where collaboration with experimentalists is expected. The project involves interactions with computational scientists working at various scales, from quantum chemists to continuum mechanicians. Experience with particle simulation techniques (e.g., molecular dynamics, Monte Carlo, dissipative particle dynamics) is required. Familiarity with bottom-up coarse-graining methods such as structure matching, force-matching etc. is a plus. The position will require substantial modifications of large parallel molecular simulation software written in C++, Fortran95, and previous experience in scientific software development is essential. Qualified candidates should have received their doctorates in one of the following areas of study: Chemical or Mechanical Engineering, Chemistry, Physics, or Materials Science. Salary is commensurate with experience and skills, but approximately $6500/month plus health insurance allowance. Publication in the open literature and attendance at national and international meetings is expected. Opportunities exist for interactions with other government laboratories and university researchers. The position is available at the Aberdeen Proving Ground, MD, which is 20 minutes north of Baltimore, and offers easy access to Washington D.C., Philadelphia, and New York City. Candidates must be U.S. citizens. For more information please contact: -- Dr. Sergey Izvekov U.S. Army Research Laboratory Weapons and Materials Research Directorate Aberdeen Proving Ground, MD 21005 sergiy.izvyekov@mail.mil - -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] md.log interpretation
Dear gromacs users, I've just finished my NVT equilibration in implicit solvent. From md.log, i see that most of time were used to calculate Forces (of Born force chain rule). Could someone explain to me why calculating it takes so long? mdp setting: integrator=md dt=0.004 nstep=250 bd-frict=50 rlist=5 rvdw=5 rcoulomb=5 nstlist=40 implicit-solvent=GBSA gb-alogarithm=still nstgbradii=40 gbradii=5 gb-epsilon-solvent=80 gb-salt-conc=0.2 sa-algorithm=ace-approximation sa-surface-tension=2.05 constraints=all-bonds constraints-algorithm=LINCS lincs-order=12 md.log M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernelsNxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) VF=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops - NB VdW [VF] 32677.013279 32677.013 0.0 NB VdW [F] 1740991.575264 1740991.575 0.3 NB VdW Elec. [VF] 1192677.312698 1192677.313 0.2 NB VdW Elec. [F] 106409048.599622 106409048.60017.9 1,4 nonbonded interactions 20035.628466 1803206.562 0.3 Born radii (Still) 1999216.23274293963162.93915.8 Born force chain rule 25548182.811729 *383222742.176*64.4 NS-Pairs 64906.572700 1363038.027 0.2 CG-CoM 205.506576 616.520 0.0 Propers 15168.313980 3473543.901 0.6 Impropers 637.980588 132699.962 0.0 Pos. Restr. 3830.053530 191502.676 0.0 Virial 82.6954711488.518 0.0 Stop-CM 82.214752 822.148 0.0 Calc-Ekin 822.011152 22194.301 0.0 Lincs 4696.969329 281818.160 0.0 Lincs-Mat 229529.791548 918119.166 0.2 Constraint-V 9393.938658 75151.509 0.0 Constraint-Vir 46.9739791127.375 0.0 Virtual Site 3 615.868824 22787.146 0.0 Virtual Site 3fd 791.205144 75164.489 0.0 Virtual Site 3fad 168.761208 29701.973 0.0 Virtual Site 3out 1893.632256 164746.006 0.0 Virtual Site 4fdn 576.418152 146410.211 0.0 (null) 476.315439 0.000 0.0 - Total 595265438.267 100.0 - R E A L C Y C L E A N D T I M E A C C O U N T I N G On 1 MPI rank Computing: Num Num CallWall time Giga-Cycles Ranks Threads Count (s) total sum% - Vsite constr. 111085001 96.421385.432 0.2 Neighbor search11 27126 915.964 3661.462 2.1 Force 111085001 *39317.742* 157168.118 91.3 Vsite spread 111095852 142.563569.880 0.3 Write traj.11 11030 425.764 1701.942 1.0 Update 111085001 96.742386.714 0.2 Constraints1110850011311.720 5243.449 3.0 Rest 766.404 3063.612 1.8 - Total 43073.320 172180.608 100.0 - Core t (s) Wall t (s)(%) Time:41985.82843073.320 97.5 11h57:53 (ns/day)(hour/ns) Performance:8.7062.757 Finished mdrun on rank 0 Tue Nov 4 03:27:26 2014 I know, for someone this question is less important, but for me performance is important. -- Thanks My Best Regards, Nizar Medical Faculty of Brawijaya University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
[gmx-users] Dr.Lemkul's Umbrella Sampling Tutorial - grompp note on leap frog/Nose-Hoover
Dear Users I am following the Umbrella Sampling tutorial by Dr. Lemkul. I am using GROMACS version 4.5.6. In step 6 of the tutorial where the umbrella sampling simulations are done for each of the extracted configurations based on COM distance sampling from 0.5 - 5.0 nm along z axis , I have 27 sets. For each set I need to do a short NPT equilibration and an Umbrella run. While running grompp for the 1st configuration before the NPT equilibration the terminal showed the following message : NOTE 1 [file md_umbrella.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 My question is how will this affect my simulations ? Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Dr.Lemkul's Umbrella Sampling Tutorial - grompp note on leap frog/Nose-Hoover
On 11/3/14 7:37 PM, Agnivo Gosai wrote: Dear Users I am following the Umbrella Sampling tutorial by Dr. Lemkul. I am using GROMACS version 4.5.6. In step 6 of the tutorial where the umbrella sampling simulations are done for each of the extracted configurations based on COM distance sampling from 0.5 - 5.0 nm along z axis , I have 27 sets. For each set I need to do a short NPT equilibration and an Umbrella run. While running grompp for the 1st configuration before the NPT equilibration the terminal showed the following message : NOTE 1 [file md_umbrella.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 My question is how will this affect my simulations ? It's an innocuous message. There are inherent limitations in compatibility of various algorithms and options. Notes are simply FYI. Warnings and errors indicate problems. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] bennet acceptance ratio
I didn't write the g_bar script, so I can't answer all of the questions about it. Equation 3 in that paper is a general equation true for any weight function alpha. It is not Bennett's acceptance ratio. Equation 4 is the one that's actually Bennett's equations, which chooses an alpha that gives a minimum variance answer. So you'll have to ask others about the exact usage of g_mbar. The tutorials on the Alchemistry.org web page show how to use the tool I wrote for analyzing free energy calculations with gromacs. Gromacs has plenty of functionality for printing out the energy differences between states. On Wed, Oct 29, 2014 at 8:03 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear Prof.Shirts, I have a question about your paper titled An Introduction to Best Practices in Free Energy Calculations.There are two equation (equation 3 and equation 4) of Bennet Acceptance Ratio in your paper. Which equation does Gromacs g_bar tool use from your paper? If it uses equation 3, then g_bar computes potential energy difference between two states. This potential energy difference means free energy difference between two states? Also I saw the same equation on alchemistry.org Another interesting thing, the dhdl.xvg files includes dh/dl values. And when g_bar calculates the free energy, it uses these files (dHdl.xvg). Whereas g_bar needs the potential energy differences between states/window? H=U+K, where H:Hamiltonian, U:Potential energy, T:Kinetic energy. You know g_bar gives it(Delta-G) on output screen. T=3/2kT, T=constant temperature, then H=U right. Then dH equals to dU? Thanks in advance -- Ahmet Yıldırım -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Genbox question
Dear Users, I am trying to build some starting structures of lipid bilayers for MD using genbox to add waters. For some reasons I have already equilibrated my lipids in a water box previously so it no longer looks like a perfect rectangle, there are “flying tails at the edges. However I still want to build a typical bilayer-in-water model in which water only appears above and below the bilayer (but not asides) and it should be able to introduce a periodic boundary condition in the x-y plane (assuming the bilayer’s normal is along the z-axis) afterwards. The problem is as I could not accurately define the dimensions of my equilibrated lipids anymore, how could genbox be used to fill the box as what I expected? I will greatly appreciate it if anyone could share your experience on this. Cheers, Kevin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulating Multiple Solute Particles
Thanks for your reply. However, I'm still confused. I thought that the command: #include oplsaa.ff/tip3p.itp is a call to the opls-aa force field. If this is not the correct way to include the force field parameters, how should I do that? Regards, Nathan Houtz - Original Message - From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Sent: Monday, November 3, 2014 12:44:52 PM Subject: Re: [gmx-users] Simulating Multiple Solute Particles On 11/3/14 12:50 AM, Nathan K Houtz wrote: Sorry everybody, I accidentally unsubscribed from the mailing list and missed my last response. Dr. Lemkul posted a message but I can't reply directly to it, so here's what he said: Your topology is constructed incorrectly, but without seeing it in its entirety, it is impossible to say. Please post the file for download somewhere and provide a link, otherwise copy and paste its entire contents into a reply if the message will be small enough. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul Thank you Justin! I think it's easier to just paste it here. This is my topol.top file: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.5 [ atomtypes ] ;nameat.num mass charge ptype sigma epsilon CH3 15 15.035000.000 A 0.39100 0.66944 ;united atom Methyl [C-CH3] C 12 12.011000.000 A 0.35000 0.27614 ;C [R3CCOO-] (first carbon) CM 12 12.011000.000 A 0.37500 0.43932 ;carboxyl C [R-(C=O)-OH] O8 15.999400.000 A 0.30800 0.71128 ;carboxyl O [C-O-H] OM8 15.999400.000 A 0.29600 0.87864 ;carbonyl O [C=O] H11.007940.000 A 0.0 0.0 ;carboxyl H [C-O-H] OW8 15.999400.000 A 0.31660 0.65000 HW11.007940.000 A 0.0 0.0 [ moleculetype ] ; Namenrexcl TETR3 [ atoms ] ; nrtype resnr residuatomcgnr charge mass 1 CH3 1TETR C1 1 0 15.03500 2 C 1TETR C2 1 0 12.01100 3 C 1TETR C3 1 0 12.01100 4 CM 1TETR C4 1 0.38 12.01100 5 OM 1TETR O1 1 -0.38 15.99940 6 O 1TETR O2 1 -0.40 15.99940 7 H 1TETR H4 1 0.401.00794 [constraints] ; i j funct distance 1 2 10.14550 2 3 10.11780 3 4 10.14420 4 5 10.12040 4 6 10.13100 6 7 10.89000 ; Include SPC water topology #include oplsaa.ff/tip3p.itp Here's your problem. Look at the contents of tip3p.itp: [ atoms ] ; idat type res nr residu name at name cg nr charge 1 opls_111 1 SOL OW 1 -0.834 2 opls_112 1 SOL HW1 10.417 3 opls_112 1 SOL HW2 10.417 It uses OPLS-AA atom types, but you haven't defined what those are because nothing above calls the OPLS-AA force field. Hence, grompp dies because it does not know how to assign nonbonded parameters to opls_111 or opls_112. [ system ] Tetrolic Acid in water [ molecules ] Tetrolic Acid 500 SOL 5481 I made the file myself, so I hope I didn't make any syntax errors. I discovered with the .gro file that the spacing is very important since gromacs doesn't use delimiters but allows only a fixed number of characters for each entry. Is the .top file the same way? I just used a template from some example file and tried to make the numbers fit appropriately under the headings. If it's not correct, why didn't gromacs complain when I solvated it? Doesn't it read in the topology file then as well? Topologies do not have the same formatting requirements. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201
