Re: [gmx-users] (no subject)
If you aren't adding anything too big, or to much of them, then take the final frame, use gmx insert-molecules (probably with a reduced vdw radius so they fit in) to put the additional molecule(s) in, perform standard pre production run energy minimisation etc, then off it goes again. Why can't you start two separate systems, one without, and one with? That would be a more robust way to do it. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 10 Jul 2018 at 21:22, Soham Sarkar wrote: > > Dear all, > I am planning to do a simulation where after 50ns of simulation I want to > add some other chemicals in the system and continue it for another 50ns, so > that I can have the effect of that chemicals exclusively before and after > adding it to the system.Is it at all possible? If yes please tell me the > protocol/ commands or give me some references where this type of simulation > is used. Thanks in advance. > -Soham > -- > 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.
Re: [gmx-users] Making group of different atoms
Using gmx make_ndx - 0 & a 1566 1567 1569 1571 1574 1579 The script has some help on how each of the options work too, so please read those. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Wed, 11 Jul 2018 at 03:09, Chetan Puri wrote: > > Can someone guide me in how to make a group for atoms number 1566, 1567, > 1569,1571,1574&1579, which all belong to a tyrosine residue number 128 of > protein. > > Since I need to measure distance between two groups (ligand and protein) > > > Regards, > Chetan > -- > 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.
Re: [gmx-users] Energy minimization of solvated MOFs.
Have you visualised the system to see what it is about that water that is generating such a high force? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Wed, 11 Jul 2018 at 00:57, Nagasree Garapati wrote: > > > Hi > > > I am trying to run some simulations on Metal-Organic frameworks like ZIF-8. I > have obtained both structure file (from CCDC) and forcefield data from > literature and I was able to successfully run energy minimization, and > equilibirum MD (NVT and NPT) simulations on the crystal structure of MOF. But > when I tried to perform energy minimization for a system of MOF in water (by > putting MOF in a box and solvating using gmx solvate), I am getting following > message and forces are very high on water molecules. I am not how to overcome > this problem, any thoughts are appreciated. > > > "Energy minimization has stopped, but the forces have not converged to the > requested precision Fmax < 5 (which may not be possible for your system). It > stopped because the algorithm tried to make a new step whose size was too > small, or there was no change in the energy since last step. Either way, we > regard the minimization as converged to within the available machine > precision, given your starting configuration and EM parameters. > > writing lowest energy coordinates. > > Steepest Descents converged to machine precision in 95 steps, > but did not reach the requested Fmax < 5. > Potential Energy = -3.38556029741624e+13 > Maximum force = 2.45386477264935e+25 on atom 306 > Norm of force = 1.49337454338593e+24" > > > > Thank You > > > > With Regards > Nagasree Garapati > Research Assistant Professor > Dept of Chemical and Biomedical Engineering > West Virginia University > PO Box 6102 > Morgantown, WV 26506-6102 > 304 293-5028(O) > 304 276-3674(M) > > -- > 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] Help
Hello, I have the next problem: [ 1%] No patch step for 'fftwBuild' [ 1%] No update step for 'fftwBuild' [ 1%] Performing configure step for 'fftwBuild' checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... configure: error: unsafe srcdir value: '/home/maximiliano/Proyecto Final/gromacs-2018/build/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild' src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make:109: recipe for target 'src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-configure' failed make[2]: *** [src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-configure] Error 1 CMakeFiles/Makefile2:1440: recipe for target 'src/contrib/fftw/CMakeFiles/fftwBuild.dir/all' failed make[1]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2 Makefile:162: recipe for target 'all' failed make: *** [all] Error 2 What can I do for it? Thank you. Best regards. -- 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] Any configuration for enabling thread-MPI?
Hi, The manual says: GROMACS can run in parallel on multiple cores of a singleworkstation using its built-in thread-MPI. No user action is requiredin order to enable this. However, that may not be correct because I get this error Command line: gmx_mpi mdrun -v -ntmpi 2 -ntomp 4 -nb gpu -deffnm nvt4 Back Off! I just backed up nvt4.log to ./#nvt4.log.17# Reading file nvt4.tpr, VERSION 2018 (single precision) --- Program: gmx mdrun, version 2018 Source file: src/gromacs/taskassignment/resourcedivision.cpp (line 680) Fatal error: Setting the number of thread-MPI ranks is only supported with thread-MPI and GROMACS was compiled without thread-MPI The configuration command I used is cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_MPI=on Any thought? Regards, Mahmood -- 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] Making group of different atoms
Can someone guide me in how to make a group for atoms number 1566, 1567, 1569,1571,1574&1579, which all belong to a tyrosine residue number 128 of protein. Since I need to measure distance between two groups (ligand and protein) Regards, Chetan -- 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] Energy minimization of solvated MOFs.
Hi I am trying to run some simulations on Metal-Organic frameworks like ZIF-8. I have obtained both structure file (from CCDC) and forcefield data from literature and I was able to successfully run energy minimization, and equilibirum MD (NVT and NPT) simulations on the crystal structure of MOF. But when I tried to perform energy minimization for a system of MOF in water (by putting MOF in a box and solvating using gmx solvate), I am getting following message and forces are very high on water molecules. I am not how to overcome this problem, any thoughts are appreciated. "Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 5 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. writing lowest energy coordinates. Steepest Descents converged to machine precision in 95 steps, but did not reach the requested Fmax < 5. Potential Energy = -3.38556029741624e+13 Maximum force = 2.45386477264935e+25 on atom 306 Norm of force = 1.49337454338593e+24" Thank You With Regards Nagasree Garapati Research Assistant Professor Dept of Chemical and Biomedical Engineering West Virginia University PO Box 6102 Morgantown, WV 26506-6102 304 293-5028(O) 304 276-3674(M) -- 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] (no subject)
Dear all, I am planning to do a simulation where after 50ns of simulation I want to add some other chemicals in the system and continue it for another 50ns, so that I can have the effect of that chemicals exclusively before and after adding it to the system.Is it at all possible? If yes please tell me the protocol/ commands or give me some references where this type of simulation is used. Thanks in advance. -Soham -- 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] GROMACS- suggestion for GPU buying
Hello Developers! Hope you are doing well! We are interested in buying new GPU card for simulating relatively big protein systems (more than 300K atoms) using GROMACS latest version. Currently, we have one P100 card (with 16 "real" cpu cores) that provides a good speed of around 10 ns/day for that system size. We were wondering if there is any recommendation/experience with other cards that will speed up the simulation time. Specifically, V100 PCIE, TITAN-V ,or GTX-1080TI. Many thanks, Malkeet -- Thanks & Warm Regards Malkeet S. Bahia, PhD Post Doctoral Fellow at the lab of Prof. Hanoch Senderowitz PBC Indo-Israel Post-doc fellowship Dept. of Chemistry, Building 211, Room no. 211 Bar Ilan University, Ramat Gan, 5290002, ISRAEL Mobile: +91-9815988501 (India, watts app only) +972-584553434 (Israel number) -- 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] (no subject)
Dear all, I am planning to do a simulation where after 50ns of simulation I want to add some other chemicals in the system and continue it for another 50ns, so that I can have the effect of that chemicals exclusively before and after adding it to the system.Is it at all possible? If yes please tell me the protocol/ commands or give me some references where this type of simulation is used. Thanks in advance. -Soham -- 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] ZnO Parameters
https://elib.suub.uni-bremen.de/edocs/00104076-1.pdf Page 111. On Tue, Jul 10, 2018 at 7:38 AM, wrote: > > Message: 3 > > Date: Fri, 6 Jul 2018 14:39:15 +0300 > > From: ali akg?n > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] ZnO Parameters > > Message-ID: > >hkwchrutet...@mail.gmail.com> > > Content-Type: text/plain; charset="UTF-8" > > > > Hi, > > > > You can f?nd parameters on solid state books(for example kittel) > > Thank you for your kind suggestion. However I didn't found much info from > it. > > > > > Thank you. > > > > > > 6 Tem 2018 Cum 13:09 tarihinde ?unu yazd?: > > > >> Dear Gromacs Users > >> > >> Can anyone provide me the parameters for Zinc Oxide (ZnO)? > >> > >> Thank You > >> > >> Regards > >> Zaved Hazarika > >> PhD Scholar > >> Dept.of Molecular Biology and Biotechnology > >> Tezpur University > >> India > > Thank You > > Regards > Zaved > > > * * * D I S C L A I M E R * * * > This e-mail may contain privileged information and is intended solely for > the individual named. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > immediately by e-mail if you have received this e-mail in error and destroy > it from your system. Though considerable effort has been made to deliver > error free e-mail messages but it can not be guaranteed to be secure or > error-free as information could be intercepted, corrupted, lost, destroyed, > delayed, or may contain viruses. The recipient must verify the integrity of > this e-mail message. > -- > 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] 2D density maps
Hello, I am running simulations of a membrane protein embedded in a E. coli model membrane. I want to generate 2D density plots to visualize lipids clustering and interaction with the protein, and membrane thickness. Which tool would you recommend? I have seen the tools from Luca Monticelli web site, reported in https://www.sciencedirect.com/science/article/pii/S0009308413000236?via%3Dihub. Thanks in advance Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845 yasser.almeida.hernan...@chemie.uni-hamburg.de office: Grindelallee 117, room 250c -- 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] ligpargen
Dear GROMACS users I am trying to run an md simulation on my protein in complex to a small molecule, using OPLSAA force field. then I am going to calculate binding energy using G_MMPBSA, G_MMPBSA is not able to calculate the binding energy with CHARMM36 force field, so I have to use OPLSAA. which one of topolbuild, topolgen and ligpargen programs is advised to generate topology for my small molecule? best regards Farial -- 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] y-axis [unit] for gmx analyze -dist command
Thanks Justin for the answer. Sorry, but I couldn’t understand your answer. What I can guess is may be gmx analyze is taking the entry from time series data and putting in appropriate bin, now every bin has some value which is a “integer”, now is there any further division with some number to these integer values?Thanks Yogi Sent using Zoho Mail On Mon, 09 Jul 2018 21:24:30 +0530 Justin Lemkul wrote On 7/9/18 11:38 AM, atb files wrote: > Dear users, I have two time series data files - a.xvg and b.xvg. I ran command gmx analyze -f a.xvg -dist aout.xvg gmx analyze -f b.xvg -dist bout.xvg y values for aout.xvg ranges from 0 to 0.05 and that for bout.xvg from 0 to 40, both plots are similar to the gaussian distribution. What are these plot? is it a probability distribution? then According to gmx help analyze: Option -dist produces distribution plot(s). > how come values for bout.xvg came in the range of 0 to 40? Your data occur at very different frequencies. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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.
