Re: [gmx-users] GROMACS 4.6-beta2 released
Hi Roland: Based on your test, how many speed-up you get? Yorquant 2012/12/7 Roland Schulz > On Thu, Dec 6, 2012 at 9:42 PM, Yorquant Wang wrote: > > > Hi Mark: > > There is a new instruction set architecture (*Advanced Vector > > Extensions > > * (AVX)) that can make float calculation in Intel CPU faster two times > > compared with the old instruction set. I want to know if the Gromacs > > developers have a plan to make GMX support AVX. if the GMX can support > GMX, > > I think maybe two times speed-up in GMX will be gotten immediately. > > > Yes AVX is supported. But you won't see a 2x speedup. > > Roland > > > > > > Best > > > > Yukun Wang > > PhD candidate > > Institute of Natural Sciences && College of Life Science, Shanghai Jiao > > Tong University > > Cell phone: 13621806236. > > China Shanghai > > > > > > 2012/12/7 Mark Abraham > > > > > Hi all, > > > > > > We've updated the GROMACS beta version to fix some bugs both you and we > > > found. We've also added the Adaptive resolution scheme (adResS) to our > > list > > > of new features (though we still have yet to publish a complete list of > > > those!). adResS couples two systems with different resolutions by a > force > > > interpolation, which can be used to speed-up atomistic simulations. The > > new > > > source package can be found at > > > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6-beta2.tar.gz. > Installation > > > instructions still here > > > http://www.gromacs.org/Documentation/Installation_Instructions > > > > > > Please try it out, particularly if you haven't done so already! Also, > if > > > everything is smooth sailing, please drop us a line on gmx-users just > to > > > say that. We can't tell whether silence is "worked great, nothing to > say" > > > or "haven't tried it yet". That will help us judge when things are > stable > > > enough to make a real release! > > > > > > Speaking of that, we are keen to make that final release soon. While we > > > can't pick a date yet, we promise that if you give us feedback by > > December > > > 21, then we will make a sincere effort to incorporate the results of > that > > > feedback in the final release. In particular, if it's an issue on our > > > Redmine bug report database http://redmine.gromacs.org, then it will > be > > > sure to get our attention and consideration. You'll need to register an > > > account to make a bug report (so that we can get back to you), but > that's > > > free and easy. > > > > > > We hope to release a current version of our regression test suite next > > > week, and a benchmark set soon. > > > > > > Cheers, > > > > > > Mark Abraham > > > GROMACS development manager > > > -- > > > 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 > > > > > > > > > > > -- > > Yukun Wang > > PhD candidate > > Institute of Natural Sciences && College of Life Science, Shanghai Jiao > > Tong University > > Cell phone: 13621806236. > > China Shanghai > > -- > > 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 > > > > > > > > > > > > > -- > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov > 865-241-1537, ORNL PO BOX 2008 MS6309 > -- > 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 > -- Yukun Wang PhD candidate Institute of Natural Sciences && College of Life Science, Shanghai Jiao Tong University Cell phone: 13621806236. China Shanghai -- 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] GROMACS 4.6-beta2 released
On Thu, Dec 6, 2012 at 9:42 PM, Yorquant Wang wrote: > Hi Mark: > There is a new instruction set architecture (*Advanced Vector > Extensions > * (AVX)) that can make float calculation in Intel CPU faster two times > compared with the old instruction set. I want to know if the Gromacs > developers have a plan to make GMX support AVX. if the GMX can support GMX, > I think maybe two times speed-up in GMX will be gotten immediately. > Yes AVX is supported. But you won't see a 2x speedup. Roland > > Best > > Yukun Wang > PhD candidate > Institute of Natural Sciences && College of Life Science, Shanghai Jiao > Tong University > Cell phone: 13621806236. > China Shanghai > > > 2012/12/7 Mark Abraham > > > Hi all, > > > > We've updated the GROMACS beta version to fix some bugs both you and we > > found. We've also added the Adaptive resolution scheme (adResS) to our > list > > of new features (though we still have yet to publish a complete list of > > those!). adResS couples two systems with different resolutions by a force > > interpolation, which can be used to speed-up atomistic simulations. The > new > > source package can be found at > > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6-beta2.tar.gz. Installation > > instructions still here > > http://www.gromacs.org/Documentation/Installation_Instructions > > > > Please try it out, particularly if you haven't done so already! Also, if > > everything is smooth sailing, please drop us a line on gmx-users just to > > say that. We can't tell whether silence is "worked great, nothing to say" > > or "haven't tried it yet". That will help us judge when things are stable > > enough to make a real release! > > > > Speaking of that, we are keen to make that final release soon. While we > > can't pick a date yet, we promise that if you give us feedback by > December > > 21, then we will make a sincere effort to incorporate the results of that > > feedback in the final release. In particular, if it's an issue on our > > Redmine bug report database http://redmine.gromacs.org, then it will be > > sure to get our attention and consideration. You'll need to register an > > account to make a bug report (so that we can get back to you), but that's > > free and easy. > > > > We hope to release a current version of our regression test suite next > > week, and a benchmark set soon. > > > > Cheers, > > > > Mark Abraham > > GROMACS development manager > > -- > > 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 > > > > > > -- > Yukun Wang > PhD candidate > Institute of Natural Sciences && College of Life Science, Shanghai Jiao > Tong University > Cell phone: 13621806236. > China Shanghai > -- > 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 > > > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] GROMACS 4.6-beta2 released
On 12/6/12 9:42 PM, Yorquant Wang wrote: Hi Mark: There is a new instruction set architecture (*Advanced Vector Extensions * (AVX)) that can make float calculation in Intel CPU faster two times compared with the old instruction set. I want to know if the Gromacs developers have a plan to make GMX support AVX. if the GMX can support GMX, I think maybe two times speed-up in GMX will be gotten immediately. The present release supports AVX. -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 -- 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] GROMACS 4.6-beta2 released
Hi Mark: There is a new instruction set architecture (*Advanced Vector Extensions * (AVX)) that can make float calculation in Intel CPU faster two times compared with the old instruction set. I want to know if the Gromacs developers have a plan to make GMX support AVX. if the GMX can support GMX, I think maybe two times speed-up in GMX will be gotten immediately. Best Yukun Wang PhD candidate Institute of Natural Sciences && College of Life Science, Shanghai Jiao Tong University Cell phone: 13621806236. China Shanghai 2012/12/7 Mark Abraham > Hi all, > > We've updated the GROMACS beta version to fix some bugs both you and we > found. We've also added the Adaptive resolution scheme (adResS) to our list > of new features (though we still have yet to publish a complete list of > those!). adResS couples two systems with different resolutions by a force > interpolation, which can be used to speed-up atomistic simulations. The new > source package can be found at > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6-beta2.tar.gz. Installation > instructions still here > http://www.gromacs.org/Documentation/Installation_Instructions > > Please try it out, particularly if you haven't done so already! Also, if > everything is smooth sailing, please drop us a line on gmx-users just to > say that. We can't tell whether silence is "worked great, nothing to say" > or "haven't tried it yet". That will help us judge when things are stable > enough to make a real release! > > Speaking of that, we are keen to make that final release soon. While we > can't pick a date yet, we promise that if you give us feedback by December > 21, then we will make a sincere effort to incorporate the results of that > feedback in the final release. In particular, if it's an issue on our > Redmine bug report database http://redmine.gromacs.org, then it will be > sure to get our attention and consideration. You'll need to register an > account to make a bug report (so that we can get back to you), but that's > free and easy. > > We hope to release a current version of our regression test suite next > week, and a benchmark set soon. > > Cheers, > > Mark Abraham > GROMACS development manager > -- > 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 > -- Yukun Wang PhD candidate Institute of Natural Sciences && College of Life Science, Shanghai Jiao Tong University Cell phone: 13621806236. China Shanghai -- 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] How to merge Self-made ammonia .top with tip4p
Dear Justin Thank you for reply. I added #include "ffoplsaa.itp" into top and #include "tip4p.itp"after [exclusions], as you told. Then, I could make tpr file and MD looks working. Thank you very much. Kenji - Original Message - >> From: Justin Lemkul >> To: Discussion list for GROMACS users >> Date: 2012-12-06 22:56:19 >> Subject: Re: [gmx-users] How to merge Self-made ammonia .top with tip4p >> >> >> On 12/6/12 6:09 AM, Kenji Mochizuki wrote: >> > Dear GMX users >> > >> > Could you tell me how to make the topology file for ammonia in tip4p water? >> > >> > I made topology file for ammonia by hand, as shown at end. >> > MD dose work when system has only ammonia molecules. >> > >> > For ammonia in water, >> > I had though it needed to add just two line at the top of .top file. >> > >> > #include "ffoplsaa.itp" >> > #include "tip4p.itp" >> > >> > >> > However, I got "Invalid order for directive defaults" in using grompp_d. >> > Should I add this new atoms information into ffnonbonded.itp directly ?? >> > >> >> That should not be necessary. If your [defaults] directive is properly >> commented out (as shown), you shouldn't get this error. >> >> The order of inclusion is important. You have to define all force >> field-level >> directives (e.g., [defaults], [atomtypes], etc) before you can define any >> [moleculetypes], so you can't #include "tip4p.itp" until after the ammonia >> parameters, since you're introducing new [atomtypes] for that molecule. The >> easiest solution is simply to move that #include statement right after the >> end >> of the ammonia [moleculetype] definition (see below). >> >> > >> > ;[ defaults ] >> > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ >> > ;1 2 yes 0.5 0.8333 >> > [ atomtypes ] >> > ;name bond_typemasscharge ptype sigma epsilon >> > FNFN 0. 0. A 3.39000e-01 1.414192e+00 >> > FHFH 0. 0. A 0.0e+00 0.0e+00 >> > [ moleculetype ] >> > ; Namenrexcl >> > AM 3 >> > [ atoms ] >> > ; nr type resnr residue atom cgnr charge mass typeB >> >chargeB >> > 1 FN 1AM N 1 -1.03500 14.00 >> > 2 FH 1AM H1 30.34500 1.00 >> > 3 FH 1AM H2 40.34500 1.00 >> > 4 FH 1AM H3 50.34500 1.00 >> > [ bonds ] >> > ; aiaj funct r k >> > 1 2 1 1.0124e-01 5.0242e+05 >> > 1 3 1 1.0124e-01 5.0242e+05 >> > 1 4 1 1.0124e-01 5.0242e+05 >> > [ pairs ] >> > ; aiaj funct >> > [ angles ] >> > ; aiajak funct theta cth >> > 2 1 3 1 1.0670e+02 6.2802e+02 >> > 2 1 4 1 1.0670e+02 6.2802e+02 >> > 3 1 4 1 1.0670e+02 6.2802e+02 >> > [ exclusions ] >> > 1 2 3 4 >> > 2 1 3 4 >> > 3 1 2 4 >> > 4 1 2 3 >> >> Add #include "tip4p.itp" here. >> >> -Justin >> >> > [ system ] >> > ammonia >> > [ molecules ] >> > AM 11 >> > >> > >> > K.Mochi >> > >> > >> >> -- >> >> >> 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 >> >> >> -- >> 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 >> >> >> National Institutes of Natural Sciences Institute for Molecular Science Kenji Mochizuki e-mail: kmo...@ims.ac.jp phone: 0564-55-7394 -- 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] add more solvent?
On 12/6/12 8:22 PM, Nur Syafiqah Abdul Ghani wrote: Dear Users, May I know after do the command genbox -cp prot_box.gro -ci solvent.gro -nmol 2000 -cs spc216.gro -p control.top -o prot_mix_sol.gro the result shows, Output configuration contains 1121788 atoms in 367835 residues Volume : 11420.4 (nm^3) Density: 1007.84 (g/l) Number of SOL molecules: 365793 I need to put the solvent mix with water with ratio approximately 80% of solvent : 20% water. From here after i done the calculation its only give 5% of solvent in water. Therefore my question is,can i add another -nmol of solvent without insert the -cs anymore? Hope you guys already facing the same problem like i do. The best approach is to do it in two steps: http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents -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 -- 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] gold-protein simulation stop by error in equilibrum step
Am 06.12.2012 21:16, schrieb Justin Lemkul: > > > On 12/6/12 3:12 PM, fatemeh ramezani wrote: >> hello >> I want to simulate gold nanoparticles with proteins. I've made a >> PDF file containing the nanoparticles and proteins, using Hayprkm >> software.then Ihave used thisPDF fileto start the simulation by >> gromacs. But in the early stage of equilibrium, I am faced with the >> following error. > advertisement < Concerning topologies and parameters: you can take a look at some of my and my collaborator's work: M. Hoefling, F. Iori, *S. Corni*, K.E. Gottschalk. Interaction of Amino Acids with the Au(111) Surface: Adsorption Free Energies from Molecular Dynamics Simulations, Langmuir 26, 8347 (2010) and F. Iori, R. Di Felice, E. Molinari, *S. Corni*, GolP: an atomistic force-field to describe the interaction of proteins with Au(111) surfaces , J. Comput. Chem., 1465 (2009). Best Martin -- 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] gold-protein simulation stop by error in equilibrum step
On 12/6/12 3:12 PM, fatemeh ramezani wrote: hello I want to simulate gold nanoparticles with proteins. I've made a PDF file containing the nanoparticles and proteins, using Hayprkm software.then Ihave used thisPDF fileto start the simulation by gromacs. But in the early stage of equilibrium, I am faced with the following error. application called MPI_Abort(MPI_COMM_WORLD, -1) - procesee 17application called MPI_Abort (MPI_COMM_WORLD, -1) - process Source code file:pme.c, line:538 Fatal error: 2 particles communicated to PME node 17 are more than 2/3 times the cut-off out of the domain decomposition cell of the This usually means that your system is not well equilibrated. I've read previous questions and it is said that the system is unstable, but how do I equilibrium the system? I'm having this trouble in equilibrium step Before beginning of MD. I equilibrate my system in 5 steps. by 5 em.mdp file that I named them em1.mdp, em2.mdp,em3.mdp, md100.mdp(temperature=100 k),md200.mdp(temperature=200k) and after these steps I do main simulation in 300k. I attached all mdp file. in md100.mdp steps, mdrun stops in middle of running and appear above error. Please note that the mailing list does not accept attachments. The failure is either due to an incorrect topology, inadequate minimization, or unstable .mdp settings. Please also consult: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -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 -- 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] gold-protein simulation stop by error in equilibrum step
hello I want to simulate gold nanoparticles with proteins. I've made a PDF file containing the nanoparticles and proteins, using Hayprkm software.then Ihave used thisPDF fileto start the simulation by gromacs. But in the early stage of equilibrium, I am faced with the following error. application called MPI_Abort(MPI_COMM_WORLD, -1) - procesee 17application called MPI_Abort (MPI_COMM_WORLD, -1) - process Source code file:pme.c, line:538 Fatal error: 2 particles communicated to PME node 17 are more than 2/3 times the cut-off out of the domain decomposition cell of the This usually means that your system is not well equilibrated. I've read previous questions and it is said that the system is unstable, but how do I equilibrium the system? I'm having this trouble in equilibrium step Before beginning of MD. I equilibrate my system in 5 steps. by 5 em.mdp file that I named them em1.mdp, em2.mdp,em3.mdp, md100.mdp(temperature=100 k),md200.mdp(temperature=200k) and after these steps I do main simulation in 300k. I attached all mdp file. in md100.mdp steps, mdrun stops in middle of running and appear above error. please help me to resolve my problem thank you Fatemeh Ramezani-- 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: help about opls-aa for thiophene
They have also the complete force field parameters under: OPLS Auxiliary topologyoplsaaff.itp if there are more paramters then in the oplsaa.ff directiory, then they have probably developed these parameters. They give this paper as a reference for the calculations. Probably something is mentioned there? Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen S. Hub, Luciano T. Costa and David van der Spoel Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant, J. Chem. Theor. Comput., 8, 61-74 (2012).DOI Greetings Thomas PS: If you reply with the whole digest, please delete all the stuff from the other questions. This makes it far easier to follow one question. Am 06.12.2012 18:21, schrieb gmx-users-requ...@gromacs.org: Dear Tomas, Thanks for your information! I look at the website you mentioned: http://virtualchemistry.org/molecules/110-02-1/index.php The *top file is available and the atom opls-aa types are assigned on *top file. But I can not find these parameters of dihedral angles from the default gmx (VERSION 4.5.5) directory of oplsaa.ff or the opls-aa (2005). For example: the parameters for dihedral of s-cw-cs-cs is missing Do you know where i can find these parameters? what versioni of opls-aa they are using? Thanks, Steven -- 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] Parametrisation of the cyclic nucleotides in Gromos force fields
Justin, Thanks again for explanation. It's interesting that above parametrization made by ATB have cased the system to crash within first ps of modeling ;) (On the contrarythe system with the ligand made by prodrg have been very stable during 100ns). I ve tried to re-parametrized my molecule by another algorithm implemented in ATB ( am1 instead of pm3 which was used in the crashed simulation). James 2012/12/6, Justin Lemkul : > > > On 12/6/12 2:39 AM, James Starlight wrote: >> Justin, >> >> Could you provide me with the example of the server where I could >> obtain Gromac's itp topologies for the charmm ff? I know many such >> servers which could be useful only for preparation systems for NAMD >> program. >> > > Google "CHARMM ligand topology in Gromacs" (without the quotes) - the first > > result is what you're looking for. > >> >> By the way recently I've made parametrization of my cGMP molecule by >> means of ATB server. In the below example you can see that the charge >> distribution is differs from the PRODRG example of that molecule which >> I've posted yesterday. Does that charge distribution more suitable for >> the 54a force field? >> > > Given that PRODRG generally produces very bad charges, just about anything > is > better ;) > > Nucleotide parameters already exist in 54A7, I don't see why you necessarily > > have to create them from scratch. In general, these charges look pretty > good, > but note that DGUA already exists and can describe most of your molecule > already. The cyclic part is the only trick, but the nucleobase parameters > should be the same in cGMP and DGUA, given the nature of Gromos96 > parameterization. > > -Justin > >> [ atoms ] >> ; nr type resnr resid atom cgnr chargemasstotal_charge >> 1NT1_N4H N21 -0.832 14.0067 >> 2 H1_N4HH2210.416 1.0080 >> 3 H1_N4HH2110.416 1.0080 ; 0.000 >> 4NR1_N4H N12 -0.715 14.0067 >> 5 H1_N4H H120.427 1.0080 >> 6 C1_N4H C220.775 12.0110 >> 7NR1_N4H N32 -0.691 14.0067 >> 8 C1_N4H C420.431 12.0110 >> 9NR1_N4H N92 -0.227 14.0067 ; 0.000 >> 10 C1_N4H C830.220 12.0110 >> 11HC1_N4HH0130.162 1.0080 >> 12 O1_N4H O63 -0.556 15.9994 >> 13 C1_N4H C630.669 12.0110 >> 14 C1_N4H C530.026 12.0110 >> 15NR1_N4H N73 -0.521 14.0067 ; 0.000 >> 16OE1_N4HO4*4 -0.429 15.9994 >> 17 CH11_N4HC1*40.429 13.0190 ; 0.000 >> 18 CH11_N4HC4*50.000 13.0190 ; 0.000 >> 19OA1_N4HO5*6 -0.422 15.9994 >> 20 P1_N4HPAQ60.971 30.9738 >> 21OM1_N4HOAR6 -0.613 15.9994 >> 22OA1_N4HO3*6 -0.382 15.9994 >> 23OA1_N4HOAS6 -0.617 15.9994 >> 24 H1_N4HH0360.497 1.0080 >> 25 CH21_N4HC5*60.319 14.0270 >> 26 CH11_N4HC3*60.247 13.0190 ; -0.000 >> 27 CH11_N4HC2*70.200 13.0190 >> 28OA1_N4HO2*7 -0.614 15.9994 >> 29 H1_N4HH8M70.414 1.0080 ; 0.000 >> >> >> >> James >> >> 2012/12/5 Justin Lemkul : >>> >>> >>> On 12/5/12 1:39 PM, James Starlight wrote: Justin, Indeed the force field is the 54a7 ( modiffied version of the 54a6). The main reason of using GROMOS ff in that case was the topology of ligands which could be easily created by means of prodrg or ATB. On other hand I've never worked with the protein-ligand complexes in charmm ff for instance. >>> >>> Well, you get out what you put in. A recent paper >>> (dx.doi.org/10.1002/jcc.23055) showed that Gromos force fields performed >>> very poorly for simulating nucleic acids. There are others, but that's >>> just >>> a recent one. If you're choosing a force field because it makes life >>> easy, >>> be prepared to defend your results if they are of poor quality or defend >>> a >>> lot of wasted time while you re-do the simulations :) >>> >>> There are servers that produce CHARMM topologies and other programs that >>> will convert AMBER topologies into Gromacs format as well. I would >>> suggest >>> you evaluate all the options available. >>> >>> By the way is there any suitable builing blocks (implemented in the rtp enties of the gromos ff) which could be used for charge assignment? >>> >>> That depends on the functional group. If it's also found in proteins, >>> yes. >>> If not, then maybe but probably not. >>> >>> >>
[gmx-users] g_analyze -oneacf
Dear users, I have a question concerning g_analyze: I have N similar time-dependent datasets, calculate autocorrelation functions using "g_analyze -f -ac -n -nosubav" and get N results. I found that the program can also be called with the option -oneacf, but was not able yet to find out, what this option is doing. The manual says "-oneacf - calculate one ACF over all sets". Does this mean that the ACF is calculated averaging over all sets during the calculation of the correlation? Or does g_analyze simply average the input or output? Thanks in advance for any help, Humphrey -- 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 104, Issue 24
Dear Tomas, Thanks for your information! I look at the website you mentioned: http://virtualchemistry.org/molecules/110-02-1/index.php The *top file is available and the atom opls-aa types are assigned on *top file. But I can not find these parameters of dihedral angles from the default gmx (VERSION 4.5.5) directory of oplsaa.ff or the opls-aa (2005). For example: the parameters for dihedral of s-cw-cs-cs is missing Do you know where i can find these parameters? what versioni of opls-aa they are using? Thanks, Steven On Thu, Dec 6, 2012 at 9:08 AM, wrote: > 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. help about opls-aa for thiophene (Thomas Schlesier) >2. How to merge Self-made ammonia .top with tip4p (Kenji Mochizuki) >3. Re: Issue building template file for Gromacs 4.6-beta1 > (Roland Schulz) >4. oplsff- need of gro and itp file -reg (venkatesh s) >5. Re: oplsff- need of gro and itp file -reg (Justin Lemkul) >6. Re: Parametrisation of the cyclic nucleotides in Gromos force > fields (Justin Lemkul) >7. Re: Asymmetry in homo dimer simulation (Justin Lemkul) > > > -- > > Message: 1 > Date: Thu, 6 Dec 2012 12:11:35 +0100 > From: Thomas Schlesier > Subject: [gmx-users] help about opls-aa for thiophene > To: > Message-ID: <50c07d67.4010...@uni-mainz.de> > Content-Type: text/plain; charset="ISO-8859-1"; format=flowed > > Have a look there: > http://virtualchemistry.org/molecules/110-02-1/index.php > > "virtualchemistry.org" is a really nice site (from David van der Spoel, > and others i think), which has many paramters for solvents for the GAFF > and OPLS force field. And also Physical properties for these. > > Greetings > Thomas > > > C4H4S. Thiophene is common compound . it seems oplss-aa does not have the > > parameters for it (such > > as dihedral angle). > > > > Any expert of opls-aa forcefield can help with ff parameters for > thiophene? > > Thanks very much! > > > > Steven > > > > -- 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] Issue building template file for Gromacs 4.6-beta1
Okay. Thanks for the fix, it worked. Hubert 2012/12/6 Roland Schulz > Hi, > > > On Thu, Dec 6, 2012 at 4:58 AM, hubert santuz >wrote: > > > > > The building/compilation of gromacs itself is working. > > But, when I try to compile the template file to create my own plugin, it > > fails. > > > Yes. I broke that for beta1. If you don't want to wait for beta2 or 3 (not > sure it'll make it into beta2). You can download a fix here: > https://gerrit.gromacs.org/#/c/1884/ > > Roland > > > -- > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov > 865-241-1537, ORNL PO BOX 2008 MS6309 > -- > 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 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] Asymmetry in homo dimer simulation
On 12/6/12 5:46 AM, Kavyashree M wrote: Sir, I also have come across several papers where they have done single simulations but in recent days most of them perform multiple trajectories for shorter period. But I am not clear how can multiple trajectories for shorter period of time compensate for single extended time simulation. See my previous post. Several trajectories, starting from independent conditions (at least random velocities if not different configurations) lead to much better sampling, and if they converge to reinforce the argument you are making, the case is vastly stronger than if one simulation happens to produce some interesting result. Just because you can do something once doesn't necessarily make it true :) -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 -- 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] How to merge Self-made ammonia .top with tip4p
On 12/6/12 6:09 AM, Kenji Mochizuki wrote: Dear GMX users Could you tell me how to make the topology file for ammonia in tip4p water? I made topology file for ammonia by hand, as shown at end. MD dose work when system has only ammonia molecules. For ammonia in water, I had though it needed to add just two line at the top of .top file. #include "ffoplsaa.itp" #include "tip4p.itp" However, I got "Invalid order for directive defaults" in using grompp_d. Should I add this new atoms information into ffnonbonded.itp directly ?? That should not be necessary. If your [defaults] directive is properly commented out (as shown), you shouldn't get this error. The order of inclusion is important. You have to define all force field-level directives (e.g., [defaults], [atomtypes], etc) before you can define any [moleculetypes], so you can't #include "tip4p.itp" until after the ammonia parameters, since you're introducing new [atomtypes] for that molecule. The easiest solution is simply to move that #include statement right after the end of the ammonia [moleculetype] definition (see below). ;[ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ ;1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon FNFN 0. 0. A 3.39000e-01 1.414192e+00 FHFH 0. 0. A 0.0e+00 0.0e+00 [ moleculetype ] ; Namenrexcl AM 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 FN 1AM N 1 -1.03500 14.00 2 FH 1AM H1 30.34500 1.00 3 FH 1AM H2 40.34500 1.00 4 FH 1AM H3 50.34500 1.00 [ bonds ] ; aiaj funct r k 1 2 1 1.0124e-01 5.0242e+05 1 3 1 1.0124e-01 5.0242e+05 1 4 1 1.0124e-01 5.0242e+05 [ pairs ] ; aiaj funct [ angles ] ; aiajak funct theta cth 2 1 3 1 1.0670e+02 6.2802e+02 2 1 4 1 1.0670e+02 6.2802e+02 3 1 4 1 1.0670e+02 6.2802e+02 [ exclusions ] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 Add #include "tip4p.itp" here. -Justin [ system ] ammonia [ molecules ] AM 11 K.Mochi -- 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 -- 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] Asymmetry in homo dimer simulation
On 12/6/12 5:26 AM, Erik Marklund wrote: 5 dec 2012 kl. 17.26 skrev Justin Lemkul: On 12/5/12 11:21 AM, Kavyashree M wrote: Sir, Thank you for your suggestions. I decided the cutoff based on RMSD convergence. I will calculate at different time intervals. Running multiple simulation is definitely the best suggestion but due to time and machine constraint it would be difficult. Instead I have two mesophilic simulations. But Is there any other way by which I can prove this point? Not using single trajectories. Your job is to convince reviewers that your work is sound. A single trajectory is not convincing, at least to any reviewer that does his or her homework :) I don't think that the use of single trajectories is necessarily "wrong", as long as they are sufficiently long. It's usually the amount of sampling that is the crucial point, no? Well, long simulations have issues too - http://dx.doi.org/10.1016/j.bpj.2010.04.062. That said, there's probably not one single answer here. I am generally leery of anyone trying to make arguments based on a single trajectory, especially one that is relatively short by modern standards. Indeed, the simulation needs to be sufficiently long to potentially observe the phenomenon of interest, and that simulation should be converged and of adequate length to collect reasonable statistics. I think, from a practical standpoint, several simulations of intermediate length will give you better insight than a single simulation of any length. Certainly in my work on amyloid peptides, multiple trajectories of considerable length are prerequisite; most other papers get (rightly) thrown out immediately. In the case of well-folded proteins whose behavior is more predictable, you can probably get more information from a single high-quality trajectory. In the present case, where a simulation of modest length is not agreeing with (presumably) experimental data, I think sampling or convergence is a major concern. Had the trajectory reproduced the expected behavior, it's less of an issue. -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 -- 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] Parametrisation of the cyclic nucleotides in Gromos force fields
On 12/6/12 2:39 AM, James Starlight wrote: Justin, Could you provide me with the example of the server where I could obtain Gromac's itp topologies for the charmm ff? I know many such servers which could be useful only for preparation systems for NAMD program. Google "CHARMM ligand topology in Gromacs" (without the quotes) - the first result is what you're looking for. By the way recently I've made parametrization of my cGMP molecule by means of ATB server. In the below example you can see that the charge distribution is differs from the PRODRG example of that molecule which I've posted yesterday. Does that charge distribution more suitable for the 54a force field? Given that PRODRG generally produces very bad charges, just about anything is better ;) Nucleotide parameters already exist in 54A7, I don't see why you necessarily have to create them from scratch. In general, these charges look pretty good, but note that DGUA already exists and can describe most of your molecule already. The cyclic part is the only trick, but the nucleobase parameters should be the same in cGMP and DGUA, given the nature of Gromos96 parameterization. -Justin [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1NT1_N4H N21 -0.832 14.0067 2 H1_N4HH2210.416 1.0080 3 H1_N4HH2110.416 1.0080 ; 0.000 4NR1_N4H N12 -0.715 14.0067 5 H1_N4H H120.427 1.0080 6 C1_N4H C220.775 12.0110 7NR1_N4H N32 -0.691 14.0067 8 C1_N4H C420.431 12.0110 9NR1_N4H N92 -0.227 14.0067 ; 0.000 10 C1_N4H C830.220 12.0110 11HC1_N4HH0130.162 1.0080 12 O1_N4H O63 -0.556 15.9994 13 C1_N4H C630.669 12.0110 14 C1_N4H C530.026 12.0110 15NR1_N4H N73 -0.521 14.0067 ; 0.000 16OE1_N4HO4*4 -0.429 15.9994 17 CH11_N4HC1*40.429 13.0190 ; 0.000 18 CH11_N4HC4*50.000 13.0190 ; 0.000 19OA1_N4HO5*6 -0.422 15.9994 20 P1_N4HPAQ60.971 30.9738 21OM1_N4HOAR6 -0.613 15.9994 22OA1_N4HO3*6 -0.382 15.9994 23OA1_N4HOAS6 -0.617 15.9994 24 H1_N4HH0360.497 1.0080 25 CH21_N4HC5*60.319 14.0270 26 CH11_N4HC3*60.247 13.0190 ; -0.000 27 CH11_N4HC2*70.200 13.0190 28OA1_N4HO2*7 -0.614 15.9994 29 H1_N4HH8M70.414 1.0080 ; 0.000 James 2012/12/5 Justin Lemkul : On 12/5/12 1:39 PM, James Starlight wrote: Justin, Indeed the force field is the 54a7 ( modiffied version of the 54a6). The main reason of using GROMOS ff in that case was the topology of ligands which could be easily created by means of prodrg or ATB. On other hand I've never worked with the protein-ligand complexes in charmm ff for instance. Well, you get out what you put in. A recent paper (dx.doi.org/10.1002/jcc.23055) showed that Gromos force fields performed very poorly for simulating nucleic acids. There are others, but that's just a recent one. If you're choosing a force field because it makes life easy, be prepared to defend your results if they are of poor quality or defend a lot of wasted time while you re-do the simulations :) There are servers that produce CHARMM topologies and other programs that will convert AMBER topologies into Gromacs format as well. I would suggest you evaluate all the options available. By the way is there any suitable builing blocks (implemented in the rtp enties of the gromos ff) which could be used for charge assignment? That depends on the functional group. If it's also found in proteins, yes. If not, then maybe but probably not. -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 -- 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 -- Justin A. Lemkul, Ph.D. Research Scienti
Re: [gmx-users] oplsff- need of gro and itp file -reg
On 12/6/12 7:06 AM, venkatesh s wrote: Respected gromacs people's, for protein and ligand complex i want use opls ff, here found mktop for ligand (external tool in gromacs web-page) but it only provide topology file only,my question is were i will get the .gro file and .itp file ? If the program provides you with a topology, then you already have an .itp file. http://www.gromacs.org/Documentation/File_Formats/.itp_File There are lots of ways to create coordinate files: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -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 -- 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] oplsff- need of gro and itp file -reg
Respected gromacs people's, for protein and ligand complex i want use opls ff, here found mktop for ligand (external tool in gromacs web-page) but it only provide topology file only,my question is were i will get the .gro file and .itp file ? Thank You -- Regards,* *S.VENKATESH, -- 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] Issue building template file for Gromacs 4.6-beta1
Hi, On Thu, Dec 6, 2012 at 4:58 AM, hubert santuz wrote: > > The building/compilation of gromacs itself is working. > But, when I try to compile the template file to create my own plugin, it > fails. Yes. I broke that for beta1. If you don't want to wait for beta2 or 3 (not sure it'll make it into beta2). You can download a fix here: https://gerrit.gromacs.org/#/c/1884/ Roland -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] How to merge Self-made ammonia .top with tip4p
Dear GMX users Could you tell me how to make the topology file for ammonia in tip4p water? I made topology file for ammonia by hand, as shown at end. MD dose work when system has only ammonia molecules. For ammonia in water, I had though it needed to add just two line at the top of .top file. #include "ffoplsaa.itp" #include "tip4p.itp" However, I got "Invalid order for directive defaults" in using grompp_d. Should I add this new atoms information into ffnonbonded.itp directly ?? ;[ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ ;1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon FNFN 0. 0. A 3.39000e-01 1.414192e+00 FHFH 0. 0. A 0.0e+00 0.0e+00 [ moleculetype ] ; Namenrexcl AM 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 FN 1AM N 1 -1.03500 14.00 2 FH 1AM H1 30.34500 1.00 3 FH 1AM H2 40.34500 1.00 4 FH 1AM H3 50.34500 1.00 [ bonds ] ; aiaj funct r k 1 2 1 1.0124e-01 5.0242e+05 1 3 1 1.0124e-01 5.0242e+05 1 4 1 1.0124e-01 5.0242e+05 [ pairs ] ; aiaj funct [ angles ] ; aiajak funct theta cth 2 1 3 1 1.0670e+02 6.2802e+02 2 1 4 1 1.0670e+02 6.2802e+02 3 1 4 1 1.0670e+02 6.2802e+02 [ exclusions ] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 [ system ] ammonia [ molecules ] AM 11 K.Mochi -- 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] help about opls-aa for thiophene
Have a look there: http://virtualchemistry.org/molecules/110-02-1/index.php "virtualchemistry.org" is a really nice site (from David van der Spoel, and others i think), which has many paramters for solvents for the GAFF and OPLS force field. And also Physical properties for these. Greetings Thomas C4H4S. Thiophene is common compound . it seems oplss-aa does not have the parameters for it (such as dihedral angle). Any expert of opls-aa forcefield can help with ff parameters for thiophene? Thanks very much! Steven -- 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] Asymmetry in homo dimer simulation
Sir, I also have come across several papers where they have done single simulations but in recent days most of them perform multiple trajectories for shorter period. But I am not clear how can multiple trajectories for shorter period of time compensate for single extended time simulation. Thank you Kavya On Thu, Dec 6, 2012 at 3:56 PM, Erik Marklund wrote: > > 5 dec 2012 kl. 17.26 skrev Justin Lemkul: > > > > > > > On 12/5/12 11:21 AM, Kavyashree M wrote: > >> Sir, > >> > >> Thank you for your suggestions. I decided the cutoff based on > >> RMSD convergence. I will calculate at different time intervals. > >> Running multiple simulation is definitely the best suggestion but > >> due to time and machine constraint it would be difficult. Instead > >> I have two mesophilic simulations. But Is there any other way > >> by which I can prove this point? > >> > > > > Not using single trajectories. Your job is to convince reviewers that > your work is sound. A single trajectory is not convincing, at least to any > reviewer that does his or her homework :) > > > > I don't think that the use of single trajectories is necessarily "wrong", > as long as they are sufficiently long. It's usually the amount of sampling > that is the crucial point, no? > > Erik > > > -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 > > > > > > -- > > 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 > > --- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:+46 18 471 6688fax: +46 18 511 755 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > > -- > 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 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] Asymmetry in homo dimer simulation
5 dec 2012 kl. 17.26 skrev Justin Lemkul: > > > On 12/5/12 11:21 AM, Kavyashree M wrote: >> Sir, >> >> Thank you for your suggestions. I decided the cutoff based on >> RMSD convergence. I will calculate at different time intervals. >> Running multiple simulation is definitely the best suggestion but >> due to time and machine constraint it would be difficult. Instead >> I have two mesophilic simulations. But Is there any other way >> by which I can prove this point? >> > > Not using single trajectories. Your job is to convince reviewers that your > work is sound. A single trajectory is not convincing, at least to any > reviewer that does his or her homework :) > I don't think that the use of single trajectories is necessarily "wrong", as long as they are sufficiently long. It's usually the amount of sampling that is the crucial point, no? Erik > -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 > > > -- > 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] Issue building template file for Gromacs 4.6-beta1
Hi everyone, First, here my system : Ubuntu 12.04 64 bits gcc : 4.6.3 cmake : 2.8.7 fftw : 3.3.3 including SSE 2 The building/compilation of gromacs itself is working. But, when I try to compile the template file to create my own plugin, it fails. First, I'm sourcing Gromacs. The building part with cmake is fine : [santuz]$ cmake .. /GROMACS version 4.6.0 found// //-- Configuring done// //-- Generating done// //-- Build files have been written to: [...]/gromacs-4.6_beta1/share/gromacs/template/cmake/ But when I try the "make" part, it fails : [santuz]$ make /[100%] Building C object CMakeFiles/template.dir/template.c.o// //In file included from [...]/gromacs-4.6_///beta1//include/gromacs/typedefs.h:69:0,// // from ///[...]//gromacs-4.6_///beta1//include/gromacs/futil.h:43,// // from ///[...]//gromacs-4.6_///beta1//include/gromacs/filenm.h:42,// // from ///[...]//gromacs-4.6_///beta1//share/gromacs/template/template.c:32:// ///[...]//gromacs-4.6_///beta1//include/gromacs/types/ifunc.h:42:24: fatal error: visibility.h : No file found// //compilation aborted.// //make[2]: *** [CMakeFiles/template.dir/template.c.o] Error 1// //make[1]: *** [CMakeFiles/template.dir/all] Error 2// //make: *** [all] Error 2/ Same problem when I try the other option : make -f Makefile.pkg The thing is that "visibility.h" is located "include/gromacs/" so if you change the path in "ifunc.h", it works but it's not a solution. Furthermore, when I compile Gromacs itself, it works perfectly. So, I don't really know why it's failing for the template. Cheers, Hubert -- Hubert SANTUZ Equipe DSIMB UMR-S 665, INSERM-Paris Diderot, INTS 6 rue Alexandre Cabanel 75015 Paris Tel : 01 44 49 31 53 -- 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
