Re: [gmx-users] gmx pdb2gmx for synthetic nucleic acid sequences
On 3/12/16 6:55 PM, fulvio ciriaco wrote: Hello, I have to simulate some non natural sequences containing sometimes both T and U nucleic acids. However pdb2gmx incorrectly detects the terminus, i.e., for a sequence like TCAUA it says Identified residue DT1 as a starting terminus. Warning: Residue RU4 in chain has different type (RNA) from starting residue DT1 (DNA). Warning: Residue DA5 in chain has different type (DNA) from starting residue DT1 (DNA). Identified residue DA3 as a ending terminus. Then it does not treat DA5 as a ending terminus, i.e. , with amber99sb-ildn ff Fatal error: Atom H3T in residue DA 5 was not found in rtp entry DA with 32 atoms while sorting atoms. Is there some way to circumvent the excessive knowledge pdb2gmx has of biological systems? Make a local copy of residuetypes.dat and set RU to DNA. pdb2gmx functions to prevent people from mixing things that shouldn't be mixed; if you are doing something strange, this is the only way to convince pdb2gmx to listen to you rather than its programming :) I attach the tertiary structure for one such sequence. The mailing list does not accept attachments, but none is necessary here. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx pdb2gmx for synthetic nucleic acid sequences
Hello, I have to simulate some non natural sequences containing sometimes both T and U nucleic acids. However pdb2gmx incorrectly detects the terminus, i.e., for a sequence like TCAUA it says Identified residue DT1 as a starting terminus. Warning: Residue RU4 in chain has different type (RNA) from starting residue DT1 (DNA). Warning: Residue DA5 in chain has different type (DNA) from starting residue DT1 (DNA). Identified residue DA3 as a ending terminus. Then it does not treat DA5 as a ending terminus, i.e. , with amber99sb-ildn ff Fatal error: Atom H3T in residue DA 5 was not found in rtp entry DA with 32 atoms while sorting atoms. Is there some way to circumvent the excessive knowledge pdb2gmx has of biological systems? I attach the tertiary structure for one such sequence. Fulvio -- 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] zero free energy of ligand in water
On 3/12/16 3:43 AM, Sana Saeed wrote: hi i have performed simple ligand only simulation (part of protein ligand binding free energy calcultaion: alchemical pathway: from complex protein and ligand simulation i got 11.43 kj/mol of delta G by using gmx bar, same result i got by using alchemical_analysis.py --> David Mobley's) but the only ligand simulation (ligand+water) i am getting zeros for all lambda states. is it fine? tahnks in advance No, that makes no sense. There should always be some amount of change in the free energy during the transformation. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem in editing .eps file of hbond
On 3/12/16 5:44 AM, tasneem kausar wrote: Dear all I have plotted the hydrogen bonds present at the interface of protein in its binary complex. I have already written the index file for the interface residues then used it for hydrogen bond calculation. There are a number of bonds at the interface. I am trying to put a cut off of 50 % for existence of hydrogen bonds in the whole trajectroy. So I want to remove the rest of hydrogen bonds of interface residues whose existence is less than 50% . For this purpose how should I edit the .eps file. Because there are a lot of data written and I am not able to understand the data that are given for x and y axis. Please solve the Issue An .eps file is an image; I wouldn't advise trying to mess with its contents to get the information you want. Everything you need should already be in the normal text output from hbond, most directly the hbmap.xpm file itself. Parse that information to get what you want. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Addendum to Question
On 3/12/16 11:51 AM, Robert Molt wrote: Thank you for clarifying the proper way to search the forums. I was perhaps unclear in what I wrote. I already *have *the converted topology and trajectory files (via Parmed). Rather, I am seeking the correct command to combine them into a binary (pursuant to the use of do_x3dna http://rjdkmr.github.io/do_x3dna/usage.html; this states I need to use a binary). Am I incorrect in thinking I need to apply some form of the gmx command to a gro trajectory file and a topology file to make a tpr file (which is a binary and thus not directly convertible from what I have)? You need to use grompp. It creates a .tpr by combining coordinates (not trajectory!), topology, and simulation instructions (which in this case are arbitrary, as you only care to do analysis) into a binary input file with a .tpr extension. -Justin I will begin examining your tutorials, Dr. Lemkul. Thank you. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Addendum to Question
Thank you for clarifying the proper way to search the forums. I was perhaps unclear in what I wrote. I already *have *the converted topology and trajectory files (via Parmed). Rather, I am seeking the correct command to combine them into a binary (pursuant to the use of do_x3dna http://rjdkmr.github.io/do_x3dna/usage.html; this states I need to use a binary). Am I incorrect in thinking I need to apply some form of the gmx command to a gro trajectory file and a topology file to make a tpr file (which is a binary and thus not directly convertible from what I have)? I will begin examining your tutorials, Dr. Lemkul. Thank you. -- Dr. Robert Molt Jr. r.molt.chemical.phys...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Building Gromacs 5.1.2
Hi, If you haven't installed it, then it isn't installed. Otherwise, you're not running on the machine you think that you're running on... Mark On Sat, Mar 12, 2016 at 3:46 PM Okoroafor, Kelechi < kelechi.okoroa...@gmail.com> wrote: > Thank you very much, Mark, I greatly appreciate your assistance. > > I have Ubuntu 14.0.4 live booting from an external hard drive. > > And if I remember correctly, before correctly completing the installation, > I had tried unsuccessfully to run “mdrun” and the command was not > recognized. > So I highly doubt that the distribution had Gromacs preinstalled. > > I shall go ahead and uninstall the currently installed version of Gromacs > and try reinstalling version 5.1.2. > > -- > 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] Building Gromacs 5.1.2
Thank you very much, Mark, I greatly appreciate your assistance. I have Ubuntu 14.0.4 live booting from an external hard drive. And if I remember correctly, before correctly completing the installation, I had tried unsuccessfully to run “mdrun” and the command was not recognized. So I highly doubt that the distribution had Gromacs preinstalled. I shall go ahead and uninstall the currently installed version of Gromacs and try reinstalling version 5.1.2. -- 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] Building Gromacs 5.1.2
Hi, That just means what it says. Be aware that some distributions provide GROMACS packages, which it sounds like you might have. Mark On Sat, Mar 12, 2016 at 1:28 PM Okoroafor, Kelechi < kelechi.okoroa...@gmail.com> wrote: > Hello, > > I attempted installing Gromacs 5.1.2 with gpu enabled on a live booted > Linux system, which did not have Gromacs previously installed. > > When I ran “mdrun -version” I saw that Gromacs 4.6.5 was installed with > gpu disabled. > > Please has this happened to anyone else? > > Would any one know what I might have done wrong in the course of building > and installing the software? > -- > 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] Query regarding energy minimization step (step 12: Water molecule starting at atom 13529 can not be settled.)
Thank you! SHRI KANT M Tech (Computational Biology) Centre for Biotechnology Anna University, Chennai 600025 On Fri, Mar 11, 2016 at 6:24 PM, Justin Lemkul wrote: > > > On 3/11/16 2:50 AM, shrikant kaushik wrote: > >> Dear all gromacs users, >>[shrikant@Ares Simulation]$ gmx-5.1.2 >> mdrun -v -deffnm em >> :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-: >> >> GROMACS is written by: >> Emile Apol Rossen Apostolov Herman J.C. BerendsenPar >> Bjelkmar >> Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian >> Fritsch >>Gerrit Groenhof Christoph Junghans Anca HamuraruVincent >> Hindriksen >> Dimitrios KarkoulisPeter KassonJiri Kraus Carsten >> Kutzner >> Per Larsson Justin A. Lemkul Magnus Lundborg Pieter >> Meulenhoff >> Erik Marklund Teemu Murtola Szilard Pall Sander Pronk >> Roland Schulz Alexey Shvetsov Michael Shirts Alfons >> Sijbers >> Peter TielemanTeemu Virolainen Christian WennbergMaarten Wolf >> and the project leaders: >> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel >> >> Copyright (c) 1991-2000, University of Groningen, The Netherlands. >> Copyright (c) 2001-2015, The GROMACS development team at >> Uppsala University, Stockholm University and >> the Royal Institute of Technology, Sweden. >> check out http://www.gromacs.org for more information. >> >> GROMACS is free software; you can redistribute it and/or modify it >> under the terms of the GNU Lesser General Public License >> as published by the Free Software Foundation; either version 2.1 >> of the License, or (at your option) any later version. >> >> GROMACS: gmx mdrun, VERSION 5.1.2 >> Executable: /usr/local/gromacs-5.1.2/bin/gmx-5.1.2 >> Data prefix: /usr/local/gromacs-5.1.2 >> Command line: >>gmx-5.1.2 mdrun -v -deffnm em >> >> >> Running on 1 node with total 4 cores, 4 logical cores >> Hardware detected: >>CPU info: >> Vendor: GenuineIntel >> Brand: Intel(R) Core(TM) i5-2400 CPU @ 3.10GHz >> SIMD instructions most likely to fit this hardware: AVX_256 >> SIMD instructions selected at GROMACS compile time: AVX_256 >> >> Reading file em.tpr, VERSION 5.1.2 (single precision) >> Using 1 MPI thread >> Using 4 OpenMP threads >> >> >> Steepest Descents: >> Tolerance (Fmax) = 1.0e+03 >> Number of steps=5 >> Step=0, Dmax= 1.0e-02 nm, Epot= 1.64486e+07 Fmax= 3.27208e+07, atom= >> 4176 >> Step=1, Dmax= 1.0e-02 nm, Epot= 1.55865e+07 Fmax= 3.13386e+07, atom= >> 4176 >> Step=2, Dmax= 1.2e-02 nm, Epot= 1.46513e+07 Fmax= 2.97319e+07, atom= >> 4176 >> Step=3, Dmax= 1.4e-02 nm, Epot= 1.36016e+07 Fmax= 2.78772e+07, atom= >> 4176 >> Step=4, Dmax= 1.7e-02 nm, Epot= 1.24230e+07 Fmax= 2.57543e+07, atom= >> 4176 >> Step=5, Dmax= 2.1e-02 nm, Epot= 1.3e+07 Fmax= 2.33503e+07, atom= >> 4176 >> Step=6, Dmax= 2.5e-02 nm, Epot= 9.67180e+06 Fmax= 2.06643e+07, atom= >> 4176 >> Step=7, Dmax= 3.0e-02 nm, Epot= 8.12309e+06 Fmax= 1.77136e+07, atom= >> 4176 >> Step=8, Dmax= 3.6e-02 nm, Epot= 6.50058e+06 Fmax= 1.45408e+07, atom= >> 4176 >> Step=9, Dmax= 4.3e-02 nm, Epot= 4.86276e+06 Fmax= 1.12217e+07, atom= >> 4176 >> Step= 10, Dmax= 5.2e-02 nm, Epot= 3.30460e+06 Fmax= 7.87434e+06, atom= >> 4176 >> Step= 11, Dmax= 6.2e-02 nm, Epot= 2.04717e+06 Fmax= 9.25255e+06, atom= >> 75560 >> Wrote pdb files with previous and current coordinates >> >> --- >> Program gmx mdrun, VERSION 5.1.2 >> Source code file: >> /usr/local/src/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555 >> >> Fatal error: >> >> step 12: Water molecule starting at atom 13529 can not be settled. >> Check for bad contacts and/or reduce the timestep if appropriate. >> >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> --- >> > > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System > > Since it's EM that's failing, the most likely problem is unreasonable > coordinates (mdrun is printing out likely locations of these nasty > interactions!). Since you've provided no other useful information about > what you're doing or what your system is, that's the best advice that can > be given. > > -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 > > ===
[gmx-users] Building Gromacs 5.1.2
Hello, I attempted installing Gromacs 5.1.2 with gpu enabled on a live booted Linux system, which did not have Gromacs previously installed. When I ran “mdrun -version” I saw that Gromacs 4.6.5 was installed with gpu disabled. Please has this happened to anyone else? Would any one know what I might have done wrong in the course of building and installing the software? -- 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] Building Gromacs 5.1.2
Hello, I attempted installing Gromacs 5.1.2 with gpu enabled on a live booted Linux system, which did not have Gromacs previously installed. When I ran “mdrun -version” I saw that Gromacs 4.6.5 was installed with gpu disabled. Please has this happened to anyone else? Would any one know what I might have done wrong in the course of building and installing the software? -- 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] problem in editing .eps file of hbond
Dear all I have plotted the hydrogen bonds present at the interface of protein in its binary complex. I have already written the index file for the interface residues then used it for hydrogen bond calculation. There are a number of bonds at the interface. I am trying to put a cut off of 50 % for existence of hydrogen bonds in the whole trajectroy. So I want to remove the rest of hydrogen bonds of interface residues whose existence is less than 50% . For this purpose how should I edit the .eps file. Because there are a lot of data written and I am not able to understand the data that are given for x and y axis. Please solve the Issue Thanks in advance -- 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] Optimal hardware for running Gromacs
Dear David, I think you will find answers to many of your questions in the following publication: http://onlinelibrary.wiley.com/doi/10.1002/jcc.24030/full Best, Carsten > On 12 Mar 2016, at 02:52, David Berquist wrote: > > I'm looking into building a desktop computer for running Gromacs > simulations. I'd like to know how I should configure it to get the best > performance possible for the price. > > One example of something I might run on this system would be: simulate an > ionic polymer of approximately 100k atoms for 1 millisecond. Coarse > grained atoms, using Martini force field. > > I would be planning to spend something under $1500 on this system. > > > > In regards to the graphics card, what factors are important? I assume that > the single precision Flop/s are a big factor, but what about memory > bandwidth(on the card itself)? > > I've noticed that Gromacs pages on GPUs tend to recommend nVidia cards, > specifically those with CUDA Compute Capability 5.2. But, AMD Radeon cards > appear to offer the same processing power for far lower prices(or > alternatively, significantly more processing power for the same price). > > For example, the nVidia GTX 970 offers 3494 GFlop/s of single precision, > and 109 GFlop/s of double precision. It currently costs $290 at Newegg. > On the other hand, the AMD Radeon R9 380 provides 3476.5 GFlop/s single > precision, and 217.3 GFlop/s of double precision. It currently costs $150 > on Newegg. > > That's practically the same single precision, and nearly double the > double-precision for around half the price. > > Or, for about the same price as the nVidia GTX 970 I could get an AMD > Radeon R9 390. It provides 5120 GFlop/s of single precision and 640 > GFlop/s of double precision. That costs $310 on Newegg. > > That is, on paper, 46.5% more single precision performance, and 487% more > double precision performance(nearly 5 times as much) for only a 6.9% higher > price. > > So, does Gromacs run a lot faster on nVidia GPUs? Would the nVidia GTX 970 > provide similar or better performance than the AMD Radeon R9 390? > > One more GPU Question; does Gromacs scale linearly across multiple graphics > cards? So, if I have two identical cards which offer 2000 GFlop/s > performance each, would they both together perform about the same as a > more-expensive single card which provides 4000GFlop/s(provided you have a > fast enough CPU, of course)? > > > > Now, how about the CPU performance? Would it be better to spend a lot of > my budget on a high-end GPU, and then go for a low cost CPU? Something > like an AMD Athlon X4 860K Kaveri Quad-Core 3.7 GHz CPU? Or would > something like that bottleneck the performance of an nVidia GTX 970 or GTX > 980? Maybe a AMD FX-6300 Vishera 6-Core 3.5 GHz? AMD FX-8300 Vishera > 8-Core 3.3GHz? > Does Intel vs AMD make any significant difference? When running Gromacs on > a system with GPU compute turned on, what sort of computing load does > Gromacs put on the CPU? Is there any commonly used CPU benchmark that can > be used to approximate relative Gromacs performance between CPUs? > > > > How important is the system RAM speed? Should I spend more of my budget > building a DDR4 system(more expensive CPU, motherboard, and RAM modules), > or would that not make a significant difference over DDR3? > > Would you happen to know what quantity of memory should be sufficient for > common Gromacs simulation runs, or runs such as the example I included > above? > > > Finally, does the speed of the hard drive impact Gromacs performance? The > options are a cheap spinning-platter hard drive(100-200MB/s sequential > write), a low-cost SSD(400-500MB/s sequential write), or a high-speed PCI-E > SSD(1000-1500MB/s sequential write). Would writing out the data(.xtc, > .trr, .edr) to a slower hard drive(100-200MB/s sequential write speed) > cause the Gromacs simulation to slow down? > I don't see any reason that a cheap spinning platter hard drive would slow > Gromacs simulations down, but I want to make sure I'm not missing > anything. > > Thank you for your time. I'd be very grateful for any information you can > give me, or direct me to. > > David Berquist > -- > 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] zero free energy of ligand in water
hi i have performed simple ligand only simulation (part of protein ligand binding free energy calcultaion: alchemical pathway: from complex protein and ligand simulation i got 11.43 kj/mol of delta G by using gmx bar, same result i got by using alchemical_analysis.py --> David Mobley's) but the only ligand simulation (ligand+water) i am getting zeros for all lambda states. is it fine? tahnks in advance Sana Saeed Khan,Research AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul, South Korea. -- 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.