Re: [gmx-users] Charmm to Gromacs itps
@Justin, thank you Justin. I will give it a try then. @Miro, sure, I will look into it, thank you. - Yogesh On Fri, 31 Jan 2020 20:24:36 +0530 Miro Astore wrote Would topotools in vmd not work in this context? I haven't used it but readabout it recently and it would seem this is the use case. Of course youalso need parameters. Wondering.Best, MiroLe sam. 1 févr. 2020 à 00:55, Justin Lemkul a écrit :>>> On 1/31/20 8:25 AM, atb files wrote:> >> >> >> > The files are given on the following server:> https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated> systems using NAMD.>> If the individual topologies are not available anywhere, just a PSF,> then you will have to write your own converter program to transform the> PSF into GROMACS .top format. PSF is very verbose so this should be> straightforward.>> -Justin>> --> ==>> Justin A. Lemkul, Ph.D.> Assistant Professor> Office: 301 Fralin Hall> Lab: 303 Engel Hall>> Virginia Tech Department of Biochemistry> 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 visithttps://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] Energy plots for specific atoms/selections
Hi, I want to get an xvg file that will show me the LJ, Coulomb, and dihedral energies on a specific set of atoms. I've tried passing a .dat file with the groups of atoms from gmx select to gmx enemat but I get an error message saying that I must not have included those groups in my mdp file. How do I incorporate them into my mdp file if I don't want specific mdp options to work on them? I cannot figure out how to retrieve the data on my groups of interest. I've tried -rerun and included an index of the atoms of interest as well If anybody has a detailed explanation, I would be grateful. Thank you, Dan -- 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] High energies after alignment of trajectory
Hi, I want to calculate the free energy difference of turning some position restraints on. Therefore I run two MD simulations, one with the restraints on the protein turned on (I’m restraining the backbone of a specific loop), in the other one I have the restraints turned off. Then I rerun the trajectories of each state with the tpr of the other state and get the free energy difference using BAR. But since the protein undergoes rotational and translational movements during the simulations this does not just give me the position restraining energy. So I tried to align the trajectories before the rerun with gmx trjconv -f prod_md.trr -o pbc.trr -s prod_md.tpr -pbc mol -center gmx trjconv -f pbc.trr -fit rot+trans -o fit.trr -s prod_md.tpr But evaluating the energies from this fitted trajectory gives me super large potential energies of the system (~e+12). Is it generally possible to use a fitted trajectory to evaluate energies? Is there something wrong in the way I did the alignment? Best, Hannah -- 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] gromacs-2020 build gcc/nvcc error
Dear Ryan, On Thu, Jan 30, 2020 at 11:31 PM Ryan Woltz wrote: > Dear Szilárd, > > Thank you so much for your help. I performed the following steps > and it seems to have built successfully, I'll let you know if it does not > run correctly as well. > > rm -r gromacs-2020/ > sudo apt-get install gcc-8 g++-8 > tar -xvzf gromacs-2020.tar.gz > cd gromacs-2020/ > mkdir build > cd build > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release > Note that you are still using the _default_ gcc installation, that is gcc 7 on Ubuntu 18.04. You should see on the first line on the console when you run cmake something like: -- The C compiler identification is GNU 7.4.0 -- The CXX compiler identification is GNU 7.4.0 which will clearly indicate the version of the compiler detected. Unless you tell cmake to use the apt-get installed gcc-8, it will not use it (and you can also verify that by inspecting the CMAKE_CXX_COMPILER string in the CMakeCache.txt file). make > make check > sudo make install > source /usr/local/gromacs/bin/GMXRC > > Lastly, when I was building in default and ran into trouble I like to build > in debug so it gives details about building and helps me identify source of > the problems or identify relevant information to pass to you so you can > better help me. I appreciate your comment about not building in debugging > mode, but is there a way to run release in verbose mode? When I had > problems with other programs I'd usually build my first time in debugger > mode so I can monitor the process, then make clean and rebuild in default. > Is there a better way to do this? > A "Debug" build (i.e. when you use CMAKE_BUILD_TYPE=Debug), is useful to compile a program for running in a debugger (like gdb). You seem to instead want a way to "debug" build-time issues. A debug build will not help in that, you will not get additional information about compilation issues. You can run "make VERBOSE=1" (regadless of the build type) with makefiles generated by cmake to get a detailed information on the commands executed during the build, but unless you have a compile- or link-time failure that you want to track down that sea of output is generally not too useful. Configure-time errors are stored by cmake in files listed after the usual "-- Configuring incomplete, errors occurred!" error (files called CMakeOutput/CMakeError.txt). > Once again you help was greatly appreciated, > > Ryan > > PS again a few notes (if you have time to comment on anything incorrect) I > have for people needing a fix in the future and maybe myself if I do this > again in a few years and forget how. > > CUDA version (nvcc --version) is 9.1. This is a little confusing to me > because you referenced CUDA 10.1 and I completely rebuilt this computer in > September 2019, so unless there is a new driver since then it should be > 10.1? I grabbed the newest drivers I could find but my computer is > outputting 9.1 so I guess that is my version. > CUDA is not (just) the drivers, it is a number of software components that allow compiling for and runnig computation on the GPU: - the CUDA toolkit, latest of which is version 10.2 (as you can see here: https://developer.nvidia.com/cuda-downloads?target_os=Linux), but the Ubuntu 18.04 repositories seem to only have 9.1 - a display driver, confusingly versioned with numbers like 418.88 or 430.35, the Ubuntu packages are called "nvidia-driver-VERSION" These two of course have to be compatible, so if you decide to download the CUDA 10.2 installer from NVIDIA, this will include a compatible driver. Be careful to completely remove the NVIDIA drivers installed from the Ubuntu repositories prior to installing sofware with the NVIDIA installer! when building gromacs and I specify gcc/g++ verison 5, 8, or 9 it fails > with the original error message regarding glibc 23.2. > > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-8 -DCUDA_HOST_COMPILER=gcc-8 > -DCMAKE_CXX_COMPILER=g++-8 -DCMAKE_C_COMPILER=/usr/bin/gcc-8 > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release > Not sure, but if you want to investigate further, I suggest to start with installing a more recent CUDA toolkit version, 9.1 is already about two years old. Cheers, -- Szilárd > Do you know why this is? When I started this adventure I just had sudo > apt-get install gcc g++ build-essentials. Then I used gcc-5 g++-5 and > specified the version in the build step, which failed. after taking that > out and running sudo apt-get install gcc-9 g++-9 it passes "CMAKE" but > fails in "make". Based on your suggestions I ran the commands at the top of > the email to which then worked. Would this have worked if I had just > installed gcc-8 g++-8 from the beginning and ran CMAKE with no
Re: [gmx-users] Charmm to Gromacs itps
Would topotools in vmd not work in this context? I haven't used it but read about it recently and it would seem this is the use case. Of course you also need parameters. Wondering. Best, Miro Le sam. 1 févr. 2020 à 00:55, Justin Lemkul a écrit : > > > On 1/31/20 8:25 AM, atb files wrote: > > > > > > > > The files are given on the following server: > https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated > systems using NAMD. > > If the individual topologies are not available anywhere, just a PSF, > then you will have to write your own converter program to transform the > PSF into GROMACS .top format. PSF is very verbose so this should be > straightforward. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 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.
Re: [gmx-users] Charmm to Gromacs itps
On 1/31/20 8:25 AM, atb files wrote: The files are given on the following server:https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated systems using NAMD. If the individual topologies are not available anywhere, just a PSF, then you will have to write your own converter program to transform the PSF into GROMACS .top format. PSF is very verbose so this should be straightforward. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 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.
Re: [gmx-users] How to use TIP4P-ICE water model
Hi, I did not fully understand what you have done. But my suggestion will be to use the pre-build tip4p.gro to build the water box and then perform the simulation with the topology of tip4p-ice and run long enough to allow the molecular system to relax, then check RDF. If the profile is not what expect, cross check the TIP4P-ICE topology file.Best regards Alessandra On Thu, Jan 30, 2020 at 10:26 AM mbhendle wrote: > Dear all, > > I want to use TIP4P-ICE water model for my simulations, but inbuilt .gro > file of TIP4P-ICE is not available in Gromacs 2018. I tried alternate > method by solvating using TIP4P model and then by changing the "itp" > file of TIP4P in topology file with that of TIP4P-ICE. > > But the result of this simulation(RDF) is very different from that of > literature. Please suggest any alternate approach. > > Thanks & Regards, > > Mangesh Bhendale > -- > 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] Charmm to Gromacs itps
The files are given on the following server:https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated systems using NAMD. -Yogesh On Thu, 30 Jan 2020 19:45:16 +0530 Justin Lemkul wrote On 1/28/20 3:35 AM, atb files wrote: > > > > @Justin: the lipid is not yet added to the charmm directory. Any script? How did you produce the original PSF? -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 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.
Re: [gmx-users] Cell Membrane Potential
Hi Frank, I have never conducted any simulation on membrane potential, but you reminded me of the fact that many molecular dynamics simulations on membrane proteins do not consider the membrane potential which is ubiquitous and versatile in biological environment. If the membrane potential is a factor in your study, as it's in voltage-gated ion channel system, please refer to previous research papers and the following links: http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#electric-fields http://manual.gromacs.org/documentation/current/reference-manual/special/electric-fields.html > -原始邮件- > 发件人: "Frank Lam" > 发送时间: 2020-01-30 03:55:17 (星期四) > 收件人: gromacs.org_gmx-users@maillist.sys.kth.se > 抄送: > 主题: [gmx-users] Cell Membrane Potential > > Hi, > > I am undergraduate student wanting to learn and use GROMACS for a project > on membrane proteins. Is altering membrane potential in a simulation > possible using GROMACS? I do apologize if this is trivial. I tried looking > at the documentation, but most of the information are currently too > challenging for me. Any guidance would be greatly appreciated. > > kind regards, > Frank > -- > 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. -- Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip: 200032, Tel: (86) 021 5492 5275 -- 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] gromacs.org_gmx-users Digest, Vol 189, Issue 80, 2. Re: Analysis with .sh file (Li, Shi)
Dear all, This is an example of a line I have been using on Gromacs 5.0.4:" echo "10" "12" | gmx rdf -f box_tot -s box-npt -n box -o Mol1 &" and this is the error message I'm receiving from Gromacs: "Error in user input: Invalid selection '10 12 ' B Near '12' B B B syntax error " Regards, Riccardo -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of gromacs.org_gmx-users-requ...@maillist.sys.kth.se Sent: jueves, 30 de enero de 2020 23:31 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: gromacs.org_gmx-users Digest, Vol 189, Issue 80 Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." Today's Topics: 1. 3D monitors (tarzan p) 2. Re: Analysis with .sh file (Li, Shi) 3. Regarding rdf and number of molecules in the FSS of tetramer (Ashma Khan) 4. Customize gromac FF for lipid parameters (Yogesh Sharma) 5. Re: Customize gromac FF for lipid parameters (Justin Lemkul) 6. Re: gromacs-2020 build gcc/nvcc error (Ryan Woltz) -- Message: 1 Date: Thu, 30 Jan 2020 14:23:59 + (UTC) From: tarzan p To: "gmx-us...@gromacs.org" Subject: [gmx-users] 3D monitors Message-ID: <2141569556.1500215.1580394239...@mail.yahoo.com> Content-Type: text/plain; charset=UTF-8 Hi all..Am looking for some good 3D monitors (either passive or active)Need suggestions for some good 3D monitors for protein structure and interactions visualization... with best wishes -- Message: 2 Date: Thu, 30 Jan 2020 09:50:09 -0500 From: "Li, Shi" To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Analysis with .sh file Message-ID: Content-Type: text/plain; charset="UTF-8" > > > Dear all, > > I have recently upgrade my Gromacs to the 2019 version from the 5.0.4 > and I found out that now that while I'm trying to use a .sh, as I was > doing in the version 5.0.4, now I'm receiving back an error since the > syntax is wrong. I'm wondering if someone could please help me. > > What is the script in your .sh file? There is not enough information to find out what goes wrong. > Regards, > > Riccardo > > > > -- > > -- Message: 3 Date: Thu, 30 Jan 2020 20:29:56 +0530 From: Ashma Khan To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Regarding rdf and number of molecules in the FSS of tetramer Message-ID: Content-Type: text/plain; charset="UTF-8" Dear user's I have calculated the rdf of urea molecules around the peptides for different concentration of urea and obtained that peak height of first solvation shell (FSS) decreases with increase in concentration of urea. After that I have calculated the number of urea molecules in FSS and found that urea molecules in the FSS increases with concentration of urea. There is no correlation between the peak height of FSS and number of urea molecules. Can anybody suggest me ? what is the reason The command I have used is gmx rdf -f md.xtc -s md.tpr -o rdf.xvg -selrpos whole_res_com -seltype whole_res_com gmx select -f md.xtc -s md.tpr -os number.xvg -select "resname URE and within 0.5 of group protein" -selrpos whole_res_com -seltype whole_res_com -- Ashma Khan Research Scholar Department of Chemistry AMU, Aligarh -- Message: 4 Date: Fri, 31 Jan 2020 01:32:43 +0530 From: Yogesh Sharma To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Customize gromac FF for lipid parameters Message-ID: Content-Type: text/plain; charset="UTF-8" Hey everyone, I have a membrane patch generated by charmm gui. I want to customize my gromac forcefield in accordance with it. I want some suggestion in extracting information from charmmff. I guess i need information to add in ffbonded and ffnonbonded files. Can someone help me with it I don't want to run simulations in charmmff -- * with regards* *Yogesh Sharma* -- Message: 5 Date: Thu, 30 Jan 2020 15:27:22 -0500 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Customize gromac FF for lipid parameters Message-ID: Content-Type: text/plain; charset=utf-8; format=flowed On 1/30/20 3:02 PM, Yogesh Sharma wrote: > Hey everyone, > I have a membrane patch generated by charmm gui. I want to customize my > gromac
