Re: [gmx-users] i have queston about partial charge zinc
In general I would say that +2 is not a good choice, since it seems to me that this is a Zinc complex. You may want to look at this: http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm you should be able to create the topology in ambertools and then convert it to gromac with acpype (https://github.com/llazzaro/acpype) -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of milad bagheri Sent: 20. september 2018 14:28 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] i have queston about partial charge zinc Hi I gonna MD simulation a protein that contained a zinc ion for build topology I used from the amber99sb force field Atomic charge is written "+2" in topology. I wanted to ask if this charge is correct or should be calculated in a different way? "PDB id 4row" sincerely -- 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] simulation crash
Hi there, I am running several independent replica of similar system but in different pose of protein-peptide. I am in NVT ensemble and the length of the simulation is 125ns (dt=2fs). Few of them are crashing with the classic error: "1 particles communicated to PME node 8 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated." I am using 36 cores or a multiple of 36 (i.e. 72, 108, and so on). The weird things is that restarting the crashed replica from the checkpoint, it starts without problem and it goes for a while (hours). Then it crashes again and so on. I have checked the last frame before the crash and I do not see structural problem. Changing the number of cores from 1 to 5 improves the things but not too much, it still crashes and restarts. IMHO, if there was a problem with the system the simulation should never restart, isn't? any clue? Hope I have been clear Best Andrea -- Andrea Spitaleri PhD Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab ISTITUTO ITALIANO DI TECNOLOGIA Via Morego 30, 16163 - Genova, Italy http://it.linkedin.com/in/andreaspitaleri https://www.researchgate.net/profile/Andrea_Spitaleri https://iit.it/andrea-spitaleri cell: +39 3485188790 ORCID: http://orcid.org/-0003-3012-3557 -- 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] bond sequence and improper angles
Hi there, I have a very quick question: in rtp file the improper definition depends on the bond sequence? I mean: [ bonds ] C1 C2 C2 C3 C3 C4 [ impropers ] C1 C4 C3 C2 is identical to this: [ bonds ] C2 C1 ; swap C3 C2 ; swap C3 C4 [ impropers ] C1 C4 C3 C2 No info in the manual. Thanks Andrea -- Andrea Spitaleri PhD Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab ISTITUTO ITALIANO DI TECNOLOGIA Via Morego 30, 16163 - Genova, Italy http://it.linkedin.com/in/andreaspitaleri https://www.researchgate.net/profile/Andrea_Spitaleri https://iit.it/andrea-spitaleri cell: +39 3485188790 ORCID: http://orcid.org/-0003-3012-3557 -- 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] Visualization of xtc file
Hi
please refer to VMD guide/manual/mailing list. You have different
options to "decrease" the motion:
1. in VMD Main there is a speed control, just move to left with mouse
or/and
2. in Graphical Representations under Trajectory tab you can increase
the number of "Trajectory Smoothing Window Size".
HTH
and
On 07/08/2017 11:38, farial tavakoli wrote:
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Dear gromacs user
I am trying to view .gro and .xtc files of my complex by VMD but when i load
first .gro and then .xtc files in vmd , it has so high motion , such that no
molecules are viewable. Would you please help me how can i view it?
ThanksFarial
Sent from Yahoo Mail for iPhone
--
Andrea Spitaleri PhD
Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy
https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems
cell: +39 3485188790
https://iit.it/andrea-spitaleri
ORCID: http://orcid.org/-0003-3012-3557
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Re: [gmx-users] Makeing movies using VMD
Hi have look to viewchange rendering and make movie options in vmd: http://www.dxulab.com/wiki/vmdviewchangerenderingtutorial On 15/03/2017 18:16, Mark Abraham wrote: Hi, I suggest you have a look at the VMD website for their documentation. THere's very likely something for this. Mark On Wed, Mar 15, 2017 at 6:14 PM Poncho Arvayo Zatarain < poncho_8...@hotmail.com> wrote: Hello gromacs user: I want to do a movie of my simulation using vmd 1.9.1. I finished my simulation and i have my tpr, xtc file, etc. How can i do the movie using vmd and algo save it and attach it for paste it in a powerpoint? I only can watch the trajectory in vmd, vut not save it and put it on a powerpoint. Do i need to use another program? Thanks -- 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. -- Andrea Spitaleri PhD Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab ISTITUTO ITALIANO DI TECNOLOGIA Via Morego 30, 16163 - Genova, Italy https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems cell: +39 3485188790 https://iit.it/andrea-spitaleri ORCID: http://orcid.org/-0003-3012-3557 -- 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] g_hbond problems
I am trying to analyze the hydrogen bonds of my simulations by g_hbond. I am using an index file where I created two groups: one with acceptor atoms (carboxylic oxygen atoms in my structure) and another group with the water molecules. I got a segmentation fault with the message: Select a group: 6 Selected 6: 'PEI_&_OC' Select a group: 3 Selected 3: 'Water' Checking for overlap in atoms between PEI_&_OC and Water Calculating hydrogen bonds between PEI_&_OC (1296 atoms) and Water (258 atoms) Found 86 donors and 1382 acceptors Reading frame 0 time 1.000 Will do grid-seach on 15x15x15 grid, rcut=0.35 Segmentation fault (core dumped) The number of donors is correct (I have 86 water molecules) but the number of acceptors is not. Please, can someone tell me what I am doing wrong? Thanks Andrea -- 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] Ris: position restraint single atom
How Larger? I used 1000 Messaggio originale Oggetto: Re: [gmx-users] position restraint single atom Da: Justin Lemkul A: gmx-us...@gromacs.org CC: On 2/15/17 9:33 AM, Andrea Spitaleri wrote: > Hi there, > > I have a dsDNA and I'd like to restraint just two atoms, O3' and O5' > respectively, in order to mimic the anchor-like to a solid support. I have > create ad hoc posre.itp file but for some reason the DNA-anchor is moving too > much from the starting position. I would expect more rigidity around the two > atoms. Does it sound strange to you? I mean, I was expecting oscillation of > the > whole DNA but keeping the anchors fixed. Are two atoms too little to get this > kind behaviour (i.e. DNA-anchor)? The constant force is 1000 kJ/mol nm^2. > > Any help/comments on this are welcome. > What about using a larger force constant? Trying to impede the motion of an entire dsDNA using only two atoms as restraints might be difficult to accomplish. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] position restraint single atom
Hi there, I have a dsDNA and I'd like to restraint just two atoms, O3' and O5' respectively, in order to mimic the anchor-like to a solid support. I have create ad hoc posre.itp file but for some reason the DNA-anchor is moving too much from the starting position. I would expect more rigidity around the two atoms. Does it sound strange to you? I mean, I was expecting oscillation of the whole DNA but keeping the anchors fixed. Are two atoms too little to get this kind behaviour (i.e. DNA-anchor)? The constant force is 1000 kJ/mol nm^2. Any help/comments on this are welcome. Thanks and -- Andrea Spitaleri PhD Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab ISTITUTO ITALIANO DI TECNOLOGIA Via Morego 30, 16163 - Genova, Italy https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems cell: +39 3485188790 https://iit.it/andrea-spitaleri ORCID: http://orcid.org/-0003-3012-3557 -- 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] position restraint single atom
Hi there, I have a dsDNA and I'd like to restraint just two atoms, O3' and O5' respectively, in order to mimic the anchor-like to a solid support. I have create ad hoc posre.itp file but for some reason the DNA-anchor is moving too much from the starting position. I would expect more rigidity around the two atoms. Does it sound strange to you? I mean, I was expecting oscillation of the whole DNA but keeping the anchors fixed. Are two atoms too little to get this kind behaviour (i.e. DNA-anchor)? The constant force is 1000 kJ/mol nm^2. Any help/comments on this are welcome. Thanks and -- Andrea Spitaleri PhD Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab ISTITUTO ITALIANO DI TECNOLOGIA Via Morego 30, 16163 - Genova, Italy https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems cell: +39 3485188790 https://iit.it/andrea-spitaleri ORCID: http://orcid.org/-0003-3012-3557 -- 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] Protein-DNA_ligand simulation.
You can think to use AMBER14SB too which contains the stable bsc0 parameters: "Uses frcmod.ff14SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA" or as Justin suggested the new bsc1 from Orozco http://www.nature.com/nmeth/journal/v13/n1/full/nmeth.3658.html http://mmb.irbbarcelona.org/BigNASim/help.php?id=download HTH and On 22/11/2016 21:24, Justin Lemkul wrote: On 11/22/16 2:06 PM, maria khan wrote: Dear Gromacs users. Can gromacs is used in Protein -DNA-ligand simulation??f it is used, which forcefield will be used.?? Just about any will work, but CHARMM and AMBER are most commonly used for systems like these. You should investigate (in the literature) the suitability of current parameter sets in light of how they might affect properties of interest (e.g. AMBER99 is a bad choice for DNA because it distorts over time, but more recent parmbsc1 is good, similarly CHARMM36 is vastly better than CHARMM27 for nucleic acids). what will be the method for that type of simulation.kindly answer me in detail. Simulating a protein-DNA complex is no different from a protein in water. You've got a biomolecule in aqueous solvent. The protocol is generally the same. -Justin -- Andrea Spitaleri PhD Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab ISTITUTO ITALIANO DI TECNOLOGIA Via Morego 30, 16163 - Genova, Italy https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems cell: +39 3485188790 https://iit.it/people/andrea-spitaleri ORCID: http://orcid.org/-0003-3012-3557 -- 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] Post-doctoral position in Computational Physics
Hi all, A post-doctoral position in Computational Physics is currently available in the Computational mOdelling of NanosCalE and bioPhysical sysTems (CONCEPT) Lab (https://beta.iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems) at IIT - Genoa (ITA) to work on the theory and modeling for molecular simulation. More information: https://beta.iit.it/careers/openings/opening/81-post-doctoral-position-in-computational-physics Best and -- Andrea Spitaleri PhD Istituto Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT LabItaliano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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] Calculate NMR shift from simulation
Hi, this task is quite challenging and up to now there are few valid protocols to quantitative correlate simulations with chemical shift calculations. Moreover you are dealing with chemical shift perturbation calculation, I mean the chemical shift variation due to either the dynamics of the system or binding of a ligand or like in your case the change of solvent. In the first case from NMR you get only the average and the correlation is hard to get with MD. As I said, you can have look to these software to calcualate a posteriori (scripting ...) the chemical shift: http://shiftx.wishartlab.com/ http://www.shiftx2.ca/ http://casegroup.rutgers.edu/qshifts/about.htm http://spin.niddk.nih.gov/bax/software/SPARTA+/ https://www.shef.ac.uk/mbb/staff/williamson/shifts Based on the last approach, you can read these papers to get more details, where the chemical shifts are studied on different solvents: http://pubs.acs.org/doi/abs/10.1021/jm701194r http://pubs.rsc.org/en/Content/ArticleLanding/2012/CE/C2CE25941A#!divAbstract http://pubs.rsc.org/en/Content/ArticleLanding/2004/CE/b407163h#!divAbstract HTH Best and Andrea Spitaleri PhD D3 - Drug Discovery & Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 Da: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] per conto di Tushar Ranjan Moharana [tusharranjanmohar...@gmail.com] Inviato: martedì 29 dicembre 2015 9.42 A: gromacs.org_gmx-users@maillist.sys.kth.se Oggetto: [gmx-users] Calculate NMR shift from simulation Hi everyone , I have the shift in peak of amide proton and amide nitrogen of my protein in various polar organic solvent (40% solvent and rest water). I have simulated the protein in same condition. There is no major structural difference observed both by CD (ellipticity) and by simulation. The shift in peak is of the order of .5 ppm for proton and 2 ppm for nitrogen (pure water vs 40% solvent). Can anybody suggest me how to correlate my simulation and observed shift? I mean which parameter I should calculate? I have calculated difference in hydrogen bonding (pure water vs 40% solvent) also number of solvent molecule within 0.4 nm. However nothing correlated with observed shift (correlation coefficient less than 0.02). Any advice is precious and I am thankful for the same. "A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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] demux.pl input file
Dear Nawel, You need to concatenate the log files of replica "0". Regards, Andrea 2015-09-02 12:16 GMT+02:00 Nawel Mele <nawel.m...@gmail.com>: > Dear Users, > > I have performed a REMD simulation on a protein with 48 replicas. I have > 400ns of REMD simulation and by consequence several restart simulation and > so several .log files: > > run1_0.log , run1_0.log run1_47.log > run2_0.log , run2_0.log run2_47.log > . > . > . > runx_0.log , runx_0.log runx_47.log > > I am interested on the lowest temperature trajectory and I want to use the > demux.pl scriot. > I have been through many similar questions in the forum but I am still > confused how to use the demux.pl script. > Should I need to concatenate all my log files like this: > > cat run1_1.log run2_1.log ... runx_1.log > run_total.log > > cat run1_0.log run1_1.log run1_2.log...run1_47.log > run2_0.log run2_1.log run2_2.log... run2_47.log ... > runx_0.log runx_1.log runx_2.log ...runx_47.log > run_total.log > > Many thanks for your help. > > Nawel > > > > > > -- > > Nawel Mele, PhD Research Student > > Jonathan Essex Group, School of Chemistry > > University of Southampton, Highfield > > Southampton, SO17 1BJ > -- > 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. > -- Andrea Pérez Villa *"Res non Verba"* -- 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] GMXPBSA
Hi, Please have look here: GMXPBSA 2.1: A GROMACS tool to perform MM/PBSA and computational alanine scanning http://www.sciencedirect.com/science/article/pii/S0010465514003154? Contact me in private if you need help Best And Il 20/lug/2015 16:19 Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl ha scritto: Dear gromacs users, I would like to run BFE calculations with gromacs. I performed MD simulations for 100ns and would like to extract snapshots from the MD and split them into the complex, protein and DNA. My question is how many sps should I extarct from the MD? and Are there any scripts available for this step? Thanks for any suggestions best regards Urszula University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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] Extending Simnulation - how analyze?
Yes!! It works very good!! Thank you, Mark!! On Jul 14, 2015, at 11:39 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Was that actually your mdrun command line? I think you need gmx mdrun -s md_0_2 -deffnm md_0_1 -cpi md_0_1 (with or without -append) to actually get appending happening. mdrun does not deduce the names of the output files from the contents of the checkpoint file. Mark On Tue, Jul 14, 2015 at 9:47 AM Andrea Spinelli spinell...@gmail.com wrote: Hi Mark, in the .log file there are this lines at the start of the extending. There are: 20587 Atoms Charge group distribution at step 50: 5190 5166 5109 5122 Initial temperature: 319.123 K Started mdrun on rank 0 Sun Jul 12 20:50:29 2015 Step Time Lambda 50 1000.00.0 On Jul 14, 2015, at 9:32 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, On Tue, Jul 14, 2015 at 8:10 AM Andrea Spinelli spinell...@gmail.com wrote: @Mark The .log report works for 2000 ps. Sure, but you need to look at the bit between 1 ns and 2 ns to find out what happened when you attempted to append. Mark @Chaban I not use grompp and the extension not create .trr files. What I have to do? On Jul 14, 2015, at 3:56 AM, V.V.Chaban vvcha...@gmail.com wrote: The no-headache route is: mv confout.gro conf.gro grompp mdrun trjcat -f *.trr -o fixed.trr On Mon, Jul 13, 2015 at 6:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What did the .log file report about your attempt to append? Mark On Mon, Jul 13, 2015 at 11:18 PM Andrea Spinelli spinell...@gmail.com wrote: Hi, I’m new user of Gromacs and I need extend a simulation of 1000ps. On Gromacs 5.0.5 I use this command line as tutorial said. gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt -append It produced the md_0_2.tpr , but when I run rms command to watch the state of RMSD, it show only first 1000 ps, not from 0 to 2000 ps. Why? What is the command I have to use? to view rmds I use this command line: gmx rms -s md_0_2.tpr -f md_0_1.xtc -o rmsd.xvg Thanks a lot. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- 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. -- 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. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- 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. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- 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
Re: [gmx-users] Extending Simnulation - how analyze?
Hi Mark, in the .log file there are this lines at the start of the extending. There are: 20587 Atoms Charge group distribution at step 50: 5190 5166 5109 5122 Initial temperature: 319.123 K Started mdrun on rank 0 Sun Jul 12 20:50:29 2015 Step Time Lambda 50 1000.00.0 On Jul 14, 2015, at 9:32 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, On Tue, Jul 14, 2015 at 8:10 AM Andrea Spinelli spinell...@gmail.com wrote: @Mark The .log report works for 2000 ps. Sure, but you need to look at the bit between 1 ns and 2 ns to find out what happened when you attempted to append. Mark @Chaban I not use grompp and the extension not create .trr files. What I have to do? On Jul 14, 2015, at 3:56 AM, V.V.Chaban vvcha...@gmail.com wrote: The no-headache route is: mv confout.gro conf.gro grompp mdrun trjcat -f *.trr -o fixed.trr On Mon, Jul 13, 2015 at 6:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What did the .log file report about your attempt to append? Mark On Mon, Jul 13, 2015 at 11:18 PM Andrea Spinelli spinell...@gmail.com wrote: Hi, I’m new user of Gromacs and I need extend a simulation of 1000ps. On Gromacs 5.0.5 I use this command line as tutorial said. gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt -append It produced the md_0_2.tpr , but when I run rms command to watch the state of RMSD, it show only first 1000 ps, not from 0 to 2000 ps. Why? What is the command I have to use? to view rmds I use this command line: gmx rms -s md_0_2.tpr -f md_0_1.xtc -o rmsd.xvg Thanks a lot. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- 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. -- 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. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- 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. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- 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] Extending Simnulation - how analyze?
Hi, I’m new user of Gromacs and I need extend a simulation of 1000ps. On Gromacs 5.0.5 I use this command line as tutorial said. gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt -append It produced the md_0_2.tpr , but when I run rms command to watch the state of RMSD, it show only first 1000 ps, not from 0 to 2000 ps. Why? What is the command I have to use? to view rmds I use this command line: gmx rms -s md_0_2.tpr -f md_0_1.xtc -o rmsd.xvg Thanks a lot. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- 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] after extending simulation
Dear all, I extend a simulation (GROMACS 5.0.5) with these command lines: convert-tpr -s md_0_1.tpr -extend 1000 -o next.tpr mdrun -s md_0_2.tpr -cpi md_0_1.cpt And now? What I have to do to view the new .gro file (i use VMD to see it) with new state of protein folding simulation? Please help me! Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- 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] after extending simulation
So, I’m ok! I can read the only one .gro file created at the first simulation as the final .gro file after all extensions. That’s right? On Jul 9, 2015, at 7:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 1:49 PM, Andrea Spinelli wrote: I’m sorry, I miss something with cut and paste command. On terminal I wrote: gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt There is no gromacs coordinate file in VMD, I have to convert a md_0_2.tpr into try or try file? The contents of md_0_1.tpr and md_0_2.tpr are identical except that the latter contains a different number of steps. When providing mdrun with a .cpt file, it carries out the run from that point, so the starting point of the run (time = 0) is always the same. The final coordinates are always written to a .gro file unless you specify a different format (which your above command does not). Whatever that file is called depends on the first run (md_0_1), because the file names are stored in the .cpt file; they will be appended to by default. The final .gro file has an appended name rather than being overwritten, IIRC. -Justin On Jul 9, 2015, at 7:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 1:25 PM, Andrea Spinelli wrote: Dear all, I extend a simulation (GROMACS 5.0.5) with these command lines: convert-tpr -s md_0_1.tpr -extend 1000 -o next.tpr mdrun -s md_0_2.tpr -cpi md_0_1.cpt And now? Well, the above sequence of commands won't do anything because (1) it's gmx convert-tpr not just convert-tpr and (2) if you create next.tpr and try to run md_0_2.tpr then mdrun will exit. What I have to do to view the new .gro file (i use VMD to see it) with new state of protein folding simulation? Load it like any coordinate file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- 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] after extending simulation
I’m sorry, I miss something with cut and paste command. On terminal I wrote: gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt There is no gromacs coordinate file in VMD, I have to convert a md_0_2.tpr into try or try file? On Jul 9, 2015, at 7:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 1:25 PM, Andrea Spinelli wrote: Dear all, I extend a simulation (GROMACS 5.0.5) with these command lines: convert-tpr -s md_0_1.tpr -extend 1000 -o next.tpr mdrun -s md_0_2.tpr -cpi md_0_1.cpt And now? Well, the above sequence of commands won't do anything because (1) it's gmx convert-tpr not just convert-tpr and (2) if you create next.tpr and try to run md_0_2.tpr then mdrun will exit. What I have to do to view the new .gro file (i use VMD to see it) with new state of protein folding simulation? Load it like any coordinate file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- 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] after extending simulation
I don’t obtain a .gro file after each extension. What is wrong? On Jul 9, 2015, at 8:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 2:10 PM, Andrea Spinelli wrote: So, I’m ok! I can read the only one .gro file created at the first simulation as the final .gro file after all extensions. That’s right? No, you should get a .gro file at the end of each run. But that's missing out on most of the information; loading the trajectory is of course more informative than any single snapshot. -Justin On Jul 9, 2015, at 7:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 1:49 PM, Andrea Spinelli wrote: I’m sorry, I miss something with cut and paste command. On terminal I wrote: gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt There is no gromacs coordinate file in VMD, I have to convert a md_0_2.tpr into try or try file? The contents of md_0_1.tpr and md_0_2.tpr are identical except that the latter contains a different number of steps. When providing mdrun with a .cpt file, it carries out the run from that point, so the starting point of the run (time = 0) is always the same. The final coordinates are always written to a .gro file unless you specify a different format (which your above command does not). Whatever that file is called depends on the first run (md_0_1), because the file names are stored in the .cpt file; they will be appended to by default. The final .gro file has an appended name rather than being overwritten, IIRC. -Justin On Jul 9, 2015, at 7:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 1:25 PM, Andrea Spinelli wrote: Dear all, I extend a simulation (GROMACS 5.0.5) with these command lines: convert-tpr -s md_0_1.tpr -extend 1000 -o next.tpr mdrun -s md_0_2.tpr -cpi md_0_1.cpt And now? Well, the above sequence of commands won't do anything because (1) it's gmx convert-tpr not just convert-tpr and (2) if you create next.tpr and try to run md_0_2.tpr then mdrun will exit. What I have to do to view the new .gro file (i use VMD to see it) with new state of protein folding simulation? Load it like any coordinate file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Andrea
Re: [gmx-users] MD simulation of metalloprotein
Hi, we have determined the Mn2+ OPLSA sigma and epsilon parameters in http://onlinelibrary.wiley.com/doi/10.1002/anie.201202032/suppinfo following the procedure reported here http://pubs.acs.org/doi/abs/10.1021/jp064835t hope it helps and On 28/04/2015 14:12, Justin Lemkul wrote: On 4/28/15 1:29 AM, Biplab Ghosh wrote: Dear All, I am a beginner in MD and started with Gromacs. I would like to simulate the dynamics of a homo-dimeric protein containing 2 Mn atoms at the active site. I would appreciate any sorts of help in this regards, e.g., please share your experience and/or relevant source in the web/published literature. Which force-filed would be appropriate? How can I take care of the metal ions? We've had reasonably good success with AMBER Mn2+ in concert with distance restraints on the ligating residues: http://www.pharmacy.manchester.ac.uk/bryce/amber -Justin -- Andrea Spitaleri PhD D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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] MMPBSA GMXPBSA 2.1
Hi Thomas, please forward your request to the GMXPBSA mailing list: https://groups.google.com/forum/#!forum/gmxpbsa probably it is a problem about the configuration Best and On 26/12/2014 08:57, Tom wrote: Dear GXM Users, Is there anyone who has the experience of GMXPBSA 2.1? I download the package and DEMO and gave a quick test of DEMO. There is always a Error report for all the 3 Examples in the DEMO. e.g. for the Example 1 - Setting the PBS queque variables 01:49:50 Generating the centered PDB structures in P53... 01:49:50 ERROR: I could not find _comp0.pdb in /home/user1/Research/Software/DEMO/EXAMPLE1/P53. Exiting... -- Thanks for the help! Thomas -- Andrea Spitaleri PhD D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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] Spacial density map
Hi, You could try to use in vmd VolMap tool in order to generate the dx isosurface. hope it helps and On 31/10/2014 00:46, Dallas Warren wrote: If you have access to 4.0.7 then you can do it, that will generate the SDF based on multiple molecules. Unfortunately, that functionality has been removed from the script in versions after that. 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 +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Stella Nickerson Sent: Friday, 31 October 2014 10:08 AM To: gmx-us...@gromacs.org Subject: [gmx-users] Spacial density map I am simulating an ionic liquid, and I want to generate a spatial density map on the anion around the cation. I want an image that looks like this: http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeConte nt.ImageService.svc/ImageService/Articleimage/2013/CP/c3cp53492h/c3cp53 492h-f4.gif That is, I want the isosurface of the cation right around one anion. The people who made that image say they used VMD, but I can't figure out how to do it. I try to use g_spatial, but I get a density map every anion in the box (a big white cloud. Not useful). First I ran: trjconv -s md.tpr -f mdDone.trr -o noPBC.trr -pbc mol -ur compact - center with the cation as the group to be centered and the entire system as the output group. Then I ran: trjconv -s md.tpr -f noPBC.trr -o fit.trr -fit rot+trans Then I ran: g_spatial -f fit.trr -s md.tpr -nab 20 (nab 20 because -nab 10 resulted in a sigmentation fault.) I also tried making an index file defining exactly one cation as it's own index group and used that as the solute. That didn't seem to change anything. -- 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. -- Andrea Spitaleri PhD D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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] Time averaged ramachandran plot
Hi,
on the fly try this using ALA1 as example (it can be any of your residues):
`grep -v '^#\|^@' rama.xvg | grep ALA1 | awk '{if($2 == 0) print $2}'
| awk -f std.awk
where std.awk contains:
{
x1 += $1
x2 += $1*$1
}
END {
x1 = x1/NR
x2 = x2/NR
sigma = sqrt(x2 - x1*x1)
if (NR 1) std_err = sigma/sqrt(NR -1)
print Number of points = NR
print Mean = x1
print Standard Deviation = sigma
print Standard Error = std_err
}
hope it helps
and
On 27/10/2014 01:21, Justin Lemkul wrote:
On 10/26/14 5:14 PM, Sanku M wrote:
Hi I plan to plot the ramachandran plot of all the dihedral angles
each of which is averaged over time-frames of trajectories. But, I
find g_rama or g_chi gives the time profile of ramachandran plot.
But, if I want to plot the time-averaged Phi.Psi angles of all
residues, is there any method to do it.ThanksSanku
It's a process than can easily be written in any scripting language
you like. You have all the data points, and you want an average. Just
post-process the output file with whatever kind of script (Perl,
Python, etc) you like.
-Justin
--
---
Andrea Spitaleri PhD
Principal Investigator AIRC
D3 - Drug Discovery Development
Istituto Italiano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
http://www.iit.it/en/d3-people/andrea-spitaleri.html
ORCID: http://orcid.org/-0003-3012-3557
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Re: [gmx-users] Time averaged ramachandran plot
replace with this:
`grep -v '^#\|^@' rama.xvg | grep ALA1 | awk '{print $2}' | awk -f
std.awk
On 27/10/2014 11:04, andrea wrote:
Hi,
on the fly try this using ALA1 as example (it can be any of your
residues):
`grep -v '^#\|^@' rama.xvg | grep ALA1 | awk '{if($2 == 0) print
$2}' | awk -f std.awk
where std.awk contains:
{
x1 += $1
x2 += $1*$1
}
END {
x1 = x1/NR
x2 = x2/NR
sigma = sqrt(x2 - x1*x1)
if (NR 1) std_err = sigma/sqrt(NR -1)
print Number of points = NR
print Mean = x1
print Standard Deviation = sigma
print Standard Error = std_err
}
hope it helps
and
On 27/10/2014 01:21, Justin Lemkul wrote:
On 10/26/14 5:14 PM, Sanku M wrote:
Hi I plan to plot the ramachandran plot of all the dihedral angles
each of which is averaged over time-frames of trajectories. But, I
find g_rama or g_chi gives the time profile of ramachandran plot.
But, if I want to plot the time-averaged Phi.Psi angles of all
residues, is there any method to do it.ThanksSanku
It's a process than can easily be written in any scripting language
you like. You have all the data points, and you want an average.
Just post-process the output file with whatever kind of script (Perl,
Python, etc) you like.
-Justin
--
---
Andrea Spitaleri PhD
Principal Investigator AIRC
D3 - Drug Discovery Development
Istituto Italiano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
http://www.iit.it/en/d3-people/andrea-spitaleri.html
ORCID: http://orcid.org/-0003-3012-3557
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Re: [gmx-users] add Mn in itp file
Hi, have look here in the supp mat. of this paper: http://onlinelibrary.wiley.com/doi/10.1002/anie.201202032/abstract Mn2+ for OPLS ff in case you needed it best and On 22/10/2014 16:13, Justin Lemkul wrote: On 10/22/14 5:09 AM, yaser wrote: hi i tried add Mn in .itp file but its need some information such as sigma and epsilon and i search for find this but i cant find this parameters .anyone knows any things about how can i add Mn in .itp file and if you know any tutorials articles about add ions . Parameters compatible with the AMBER force fields (and the associated reference) can be found at http://www.pharmacy.manchester.ac.uk/bryce/amber. -Justin -- --- Andrea Spitaleri PhD Principal Investigator AIRC D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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] binding Free energy
Hi, thanks Justin to point out our tool GMXPBSA (GMXAPBS was the old one) http://www.sciencedirect.com/science/article/pii/S0010465514002240 and new version 2.1: http://www.sciencedirect.com/science/article/pii/S0010465514003154 The link to the program is still not avaliable but you can grab it here: http://gdriv.es/gmxpbsa along with examples. For any help please consider to use our small mailing list here https://groups.google.com/forum/#!forum/gmxpbsa Best and On 23/10/2014 16:50, Justin Lemkul wrote: On 10/23/14 10:35 AM, Urszula Uciechowska wrote: Dear gromacs user, I would like to calculate Binding Free Energy Calculations for my protein-DNA complex (already run for 50ns). Is there any manual or tutorial (for more complex systems) available? See published methods like g_mmpbsa (very recent) or GMXAPBS. -Justin -- --- Andrea Spitaleri PhD Principal Investigator AIRC D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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] 2D diagram
Hi, try either ligplot or ligplot+ and On 10/09/2014 11:21, Andrei Neamtu wrote: Hi, Maybe this is not a directly related Gromacs question, but: I have performed a md simulation of a protein in water, and I want to follow for certain amino acids exposure to solvent and nearby contacting residues. Does anyone know a program for drawing synthetic 2D diagrams of interactions/contacts between a residue and its spatial neighbors from an PDB file? Many thanks, Andrei *Dr. Andrei Neamtu, PhD, Lecturer Department of Physiology Gr. T. Popa University of Medicine and Pharmacy of Iasi http://www.umfiasi.ro/ http://www.umfiasi.ro/ Str. Universitatii nr. 16 IASI, Jud. Iasi ROMANIA* -- --- Andrea Spitaleri PhD Principal Investigator AIRC D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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 trajectory movie last longer.
Hi, when you say too quickly are you referring to the noise I guess. If it is the case, you could try to filter you xtc either with g_filter in order to reduce the fluctuactions or in vmd itself you can smooth the xtc in the graphical representations - trajectory tab - trajectory smooting (2 or 3 should be enough) hope it helps and On 03/09/2014 15:35, Dawid das wrote: Dear Gromacs experts, I have a question not regarding Gromacs itself but maybe you found a solution. I have already solved this problem but not for GROMACS files. I want to make a trajectory movie using VMD, but following frames appear too quickly and it is very hard to actually see and analyze how chromophore structure changes over time. So I want to make the movie last longer and the frames to be be displayed for a longer timer. I did it for Tinker trajectory snapshots by uploading the same snapshot 5 or 7 times but how to do it with *gro and *trr files from Gromacs? Best wishes, Dawid Grabarek PS Maybe you suggest to use different prorgram? -- --- Andrea Spitaleri PhD Principal Investigator AIRC D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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 trajectory movie last longer.
I see now. sorry. you want make a movie. yes in vmd have look to change viewer render under visualization. and On 03/09/2014 15:45, Dawid das wrote: No, I don't mean noise :). What I mean is that next frame appears on the screen before I can take a good look at previous one. So imagine that you make a presentation and you change each slide after 0.1 s. You can't have a good look at it so let's say I need 2 s to have a good look. I hope now you understand better what I mean. 2014-09-03 14:41 GMT+01:00 andrea andrea.spital...@iit.it: Hi, when you say too quickly are you referring to the noise I guess. If it is the case, you could try to filter you xtc either with g_filter in order to reduce the fluctuactions or in vmd itself you can smooth the xtc in the graphical representations - trajectory tab - trajectory smooting (2 or 3 should be enough) hope it helps and On 03/09/2014 15:35, Dawid das wrote: Dear Gromacs experts, I have a question not regarding Gromacs itself but maybe you found a solution. I have already solved this problem but not for GROMACS files. I want to make a trajectory movie using VMD, but following frames appear too quickly and it is very hard to actually see and analyze how chromophore structure changes over time. So I want to make the movie last longer and the frames to be be displayed for a longer timer. I did it for Tinker trajectory snapshots by uploading the same snapshot 5 or 7 times but how to do it with *gro and *trr files from Gromacs? Best wishes, Dawid Grabarek PS Maybe you suggest to use different prorgram? -- --- Andrea Spitaleri PhD Principal Investigator AIRC D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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. -- --- Andrea Spitaleri PhD Principal Investigator AIRC D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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] MMPBSA with GROMACS: a new revised tool
Hi, Our tool has been published previously: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046902 The paper of the new release of our tool will be available soon. Best And Zhi Yue zhi...@umaryland.edu ha scritto: Hi Andrea, Thanks for your message! I noticed the manuscript published on J. Chem. Inf. Model. was released online today ( http://pubs.acs.org/doi/abs/10.1021/ci500020m). Best Shane On Sun, May 25, 2014 at 5:55 PM, andrea andrea.spital...@iit.it wrote: Dear all, We are very pleased to announce the release of GMXPBSA 2.0 tool to calculate binding free energy under the MM/PBSA approximation. This version is a complete rewrite of our previous GMXAPBS tool. This tool exploits the native GROMACS 4.5 and later version trajectories. Beyond GROMACS, you need to install only APBS program to solve the PB equations. The installation procedure is very easy, just untar the source code and that's it! This new version now reads an INPUT file where the user can set all the needed setting. Our tool can: 1. calculate MM/PBSA on a single trajectory 2. can perform CAS (Computational Alanine scanning) calculations a posteriori 3. simultaneously calculate MM/PBSA on a set of trajectories (i.e. to compare different ligands) 4. can perform interface interaction on protein-protein or protein-peptide (simultaneously CAS on the binding interface) 5. statistical analysis on the results The tool can be used upon request. Feel free to contact me. Best and -- --- Andrea Spitaleri PhD D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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. -- *Zhi Yue* Graduate Research Assistant Computer-Aided Drug Design Center School of Pharmacy University of Maryland 20 Penn St, Rm S612 Baltimore, MD 21201 Email:zhi...@umaryland.edu, zhi...@umd.edu -- 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] How to efficiently fix pbc trajectories problems for VMD using
Hi there, have look to arrange_objects.tcl in http://people.sissa.it/~xbiarnes/tools.php. That could be useful for your task. and -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Vito Genna Sent: lunedì 19 maggio 2014 17:04 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Dear Mark, Thank you for you prompt reply. Yes, indeed I was following the suggested trjconv workflow. Right you are. When I say does not work I mean that the system is stretched between two adjacent boxes showing internal bonds that run throughout the main pbc box (extremely long). Regarding the steps: Yes I already visualized the results step by step and after the 1) one trjconv fixes the bond problems but splits my protein in two distinct part (the protein contains only 1 chain) moving them in two boxes. At this point I use the -pbc nojump option that gives me the same previous problem (bond excessively long). If I could reassembly the protein after -pbc whole action I'll be completely satisfied. Any suggestion? Thank in advance. Cheers Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham [mark.j.abra...@gmail.com] Sent: Monday, May 19, 2014 4:31 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using You seem to be following http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions, which is good. But it's hard to help when we don't know what you think doesn't work means. Make sure that the things you think are whole in md_0_1.tpr actually are. Visualize your intermediate stages of 1) to see where the issue arises. If you need to, upload some pictures to a file sharing service that show what the input and unsatisfactory output was. Mark On Mon, May 19, 2014 at 3:15 PM, Vito Genna vito.ge...@iit.it wrote: Hi to everybody, My name is Vito and I would like to share with you (and discuss also) the problems that I have found during my TRJs analysis. I have a system made by: Protein + dsDNA + Ligand. I obtained my single precision trajectory in a .xtc file. Well, I'd like to analyze my TRJs using VMD due to its intrinsic velocity in calcuating (Distances, angles, RMSD and so on) but I cannot do it because I encounter a serious issue with the visualization (pbc problems as you surely know) To try to avoid the problem I've used several protocols, without success: 1) a) trjconv_mpi -f md_0_1.part0001.xtc -o md_0_1-whole.xtc -s md_0_1.tpr -pbc whole (on the entire system) b) trjconv_mpi -f md_0_1-whole.xtc -o md_0_1-nojump.xtc -s md_0_1.tpr -pbc nojump (on the entire system) c) trjconv_mpi -f md_0_1-nojump.xtc -o md_0_1-fit.xtc -s md_0_1.tpr -fit progressive (on Protein only) It does not work. 2) a) trjconv_mpi -f (as the previous one) -pbc mol -ur compact -center -o compact.xtc It does not work as well. 3) Option 2 changing the flag -pbc mol with -pbc res It does not work. New idea? New possible combo? Thanks in advance for your replies. All the best Vito Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy -- --- The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein -- 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. -- 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
Re: [gmx-users] re-sort frames by RMSD
Hi, you could try to sort rmsd.xvg as suggested previously using sort command. then extract all the frames from your trajectory (-skip 1 -sep) and then concatenate them again following the rmsd sorted. in perl/python you could exploit hash/dictionary approach to have order_id - rmsd_value fixed. hope it helps and On 28/03/2014 11:10, unitALX wrote: Hello Joao! Thanks for the info! Actually, I want to re-sort the actual frames in the trajectory. -- View this message in context: http://gromacs.5086.x6.nabble.com/re-sort-frames-by-RMSD-tp5015416p5015450.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- --- Andrea Spitaleri PhD D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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] parameters of ligand for force field OPLS
Also, have look to here: http://gromacs.5086.x6.nabble.com/after-using-ACPYPE-GROMACS-OPLS-itp-file-generated-an-atom-type-like-opls-x-with-mass-0-000-td5012336.html cheers and On 20/02/2014 22:30, Mahboobeh Eslami wrote: hi GMX users can i use acpype program for ligand preparation in simulation by gromacs? how can i produce the parameters of ligand for force field OPLS? thanks a lot -- Andrea Spitaleri PhD D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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.
