Re: [gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4
Hi Sapna, The list doesn't allow attachments. Please put them somewhere online and provide a link. The differences can be large. Can't tell if you don't know the possible range of conformations/trajectories for one Gromacs version. Did you ensure to remove jumps from the trajectories and/or make molecules whole, etc? That would be the only thing we'd be able to see from the RMSD plot anyway, whether you removed jumps or not. Otherwise it does not contain useful information (in this regard). Cheers, Tsjerk On Feb 11, 2016 05:28, "SAPNA BORAH" wrote: > Dear Mark, > > Please find attached a plot showing the RMSD difference. It is for the same > protein. > > Even if the same runs are not reproducible, my doubt is whether there can > be such a large variation in the RMSD trend. Which data should I rely on > then, it is giving me a hard time. > > I'll be grateful if you look into this. > > Thanks, > Sapna. > > Sapna Mayuri Borah > c/o Dr. A. N. Jha > Research student > Tezpur University, > India > > On Tue, Feb 9, 2016 at 1:07 PM, Mark Abraham > wrote: > > > Hi, > > > > This is quite normal. > > http://www.gromacs.org/Documentation/Terminology/Reproducibility. You > > should see a similar range of variation in the trajectories produced in > the > > two versions that are incompletely sampling the same ensemble, but one > can > > say very little about two single observed trajectories sampled from them. > > > > Mark > > > > On Tue, Feb 9, 2016 at 8:23 AM SAPNA BORAH > wrote: > > > > > Dear all, > > > > > > I have tried running the same protein in the two versions of gromacs > > 4.6.5 > > > and 5.0.4. Now, both the runs are producing entirely different results. > > > > > > The results till equilibration are same. > > > > > > After the run however, there is a total change in the production > > results. I > > > have used the same mdp files. > > > > > > I have rerun the systems and they still produce similar results in the > > same > > > version. > > > > > > The protein structure is a modelled one. > > > > > > > > > Thanks in advance. > > > Sapna. > > > > > > Sapna Mayuri Borah > > > c/o Dr. A. N. Jha > > > Research student > > > Tezpur University, > > > India > > > -- > > > 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. > -- 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] Different results for same protein's simulation in 4.6.5 and 5.0.4
Dear Mark, Please find attached a plot showing the RMSD difference. It is for the same protein. Even if the same runs are not reproducible, my doubt is whether there can be such a large variation in the RMSD trend. Which data should I rely on then, it is giving me a hard time. I'll be grateful if you look into this. Thanks, Sapna. Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Tue, Feb 9, 2016 at 1:07 PM, Mark Abraham wrote: > Hi, > > This is quite normal. > http://www.gromacs.org/Documentation/Terminology/Reproducibility. You > should see a similar range of variation in the trajectories produced in the > two versions that are incompletely sampling the same ensemble, but one can > say very little about two single observed trajectories sampled from them. > > Mark > > On Tue, Feb 9, 2016 at 8:23 AM SAPNA BORAH wrote: > > > Dear all, > > > > I have tried running the same protein in the two versions of gromacs > 4.6.5 > > and 5.0.4. Now, both the runs are producing entirely different results. > > > > The results till equilibration are same. > > > > After the run however, there is a total change in the production > results. I > > have used the same mdp files. > > > > I have rerun the systems and they still produce similar results in the > same > > version. > > > > The protein structure is a modelled one. > > > > > > Thanks in advance. > > Sapna. > > > > Sapna Mayuri Borah > > c/o Dr. A. N. Jha > > Research student > > Tezpur University, > > India > > -- > > 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.
Re: [gmx-users] complex topology file
On 2/10/16 8:34 PM, Sana Saeed wrote: please someone help me. i want to find out absolute binding free energy of protein ligand complex. fisrt i performed docking and selected best poses and then i made topology file of ligand with PRODRGserver. and then included itp file of ligand in Protein topology file (from pdb2gmx) , also made complex.gro as in tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html . can i use these complex files for MD for absolute binding free energy? in some tutorials the topology file of complex is quite differently organised. please guide me, i am following decoupling and coupling steps from http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme I already replied: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-February/103524.html -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] complex topology file
please someone help me. i want to find out absolute binding free energy of protein ligand complex. fisrt i performed docking and selected best poses and then i made topology file of ligand with PRODRGserver. and then included itp file of ligand in Protein topology file (from pdb2gmx) , also made complex.gro as in tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html . can i use these complex files for MD for absolute binding free energy? in some tutorials the topology file of complex is quite differently organised. please guide me, i am following decoupling and coupling steps from http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme Sana Saeed Khan,Teaching-Research AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul, South Korea. On Wednesday, February 10, 2016 12:54 AM, Sana Saeed wrote: hi gmx usersi want to find out absolute binding free energy of protein ligand complex. fisrt i performed docking and selected best poses and then i made topology file of ligand with PRODRGserver. and then included itp file of ligand in Protein topology file (from pdb2gmx) , also made complex.gro as in tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html . can i use these complex files for MD for absolute binding free energy? in some tutorials the topology file of complex is quite differently organised. please guide me, i am following decoupling and coupling steps from http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme Sana Saeed Khan,Teaching-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.
[gmx-users] Weird configuration when pulling rate is small
Dear list, I am pulling a triple helix using umbrella distance. When the pulling rate is 0.0004 nm/ps, the configuration is normal. However, when I decrease the pulling rate to 0.0002 nm/ps or lower, the configuration is messy (some atoms flow away from the triple helix), but the simulations run well and both the force_strain curve and the history of number of h_bonds look normal. Could anybody tell me why is that low pulling rates cause this problem? Thanks in advance, Ming -- 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] improper dihedral convention
Hi, Yes, the image seems to have been cropped poorly somehow. Hopefully I can fix it. I is an the middle and j is in the bottom left - if you zoom in the pdf you can see that only one of the letters i has a serif on the bottom. Mark On Wed, 10 Feb 2016 18:41 Parvez Mh wrote: > Dear All: > > I want to apply OPLS-UA improper dihedral to fused benzene ring. I am > confused with sequence of atoms. I went through manual 4.6.7,page 79, I > have confusion. > > * l* > | > | > * i* > / \ >/\ > / \ > * i k * > > I do not know if it is typo or correct, in manual, it use 'i' twice. > I never used improper, but what makes sense to me central atom should have > certain sequence. > > Regards > Masrul > -- > 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] Reading multiple trajectories for Gromacs analysis
Hello Anu, If you have the trajectories like 1-5 ns, 6-10 ns, 11-15 ns, etc, then you could concatenate all of them in to one single trajectory using the g_trjcat tool in gromacs an then use g_rms on it to calculate the RMSD. Hope this helps. On Wed, Feb 10, 2016 at 6:14 PM, anu chandra wrote: > Hello all, > > I just finished a 100 ns simulation using Gromacs, where I ran the > simulation with a 5 ns window (ie. now I have 20 .trr files with 5 ns data > in each). As I am quiet new to Gromacs, I just wonder how can I read all > the 20 trr files one-by-one to do some basic Gromacs analysis. For e.g if I > would like to see the change in RMSD along the 100 ns of simulation time, > how should I read the all trr files to do the calculation with g_rms? I do > aware that a small shell script will do the job, but I just wonder if there > is a little more straight way to do it in Gromacs itself. > > > Any suggestions would be highly appreciated > > Anu > -- > 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. > -- Best Regards, Ganesh Shahane -- 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] Reading multiple trajectories for Gromacs analysis
Hello all, I just finished a 100 ns simulation using Gromacs, where I ran the simulation with a 5 ns window (ie. now I have 20 .trr files with 5 ns data in each). As I am quiet new to Gromacs, I just wonder how can I read all the 20 trr files one-by-one to do some basic Gromacs analysis. For e.g if I would like to see the change in RMSD along the 100 ns of simulation time, how should I read the all trr files to do the calculation with g_rms? I do aware that a small shell script will do the job, but I just wonder if there is a little more straight way to do it in Gromacs itself. Any suggestions would be highly appreciated Anu -- 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] improper dihedral convention
Dear All: I want to apply OPLS-UA improper dihedral to fused benzene ring. I am confused with sequence of atoms. I went through manual 4.6.7,page 79, I have confusion. * l* | | * i* / \ /\ / \ * i k * I do not know if it is typo or correct, in manual, it use 'i' twice. I never used improper, but what makes sense to me central atom should have certain sequence. Regards Masrul -- 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] μVT simulations and genbox
In theory, https://github.com/GromPy/GromPy can do it (http://www.ncbi.nlm.nih.gov/pubmed/22370965), but it's old and I've never tried it. Not in the main code currently. On Wed, Feb 10, 2016 at 11:38 AM, Irem Altan wrote: > Hi, > > I have two questions: > > - Is it possible to do μVT simulations? > - When I copy vdwradii.dat to my working folder and modify it, does it affect > the MD simulations? I used it to modify the number of water molecules genbox > adds, and then ran an MD simulation without removing the vdwradii.dat file. > Would that affect anything? > > Best, > Irem > -- > 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] μVT simulations and genbox
Hi, I have two questions: - Is it possible to do μVT simulations? - When I copy vdwradii.dat to my working folder and modify it, does it affect the MD simulations? I used it to modify the number of water molecules genbox adds, and then ran an MD simulation without removing the vdwradii.dat file. Would that affect anything? Best, Irem -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs installation FTP issue
Hi, Yes, you could have simply changed the ftp:// prefix to http:// and it would have been fine. Future releases will likely offer both styles of link. The regressiontest download is only available with http for now, so your problem there was not related to FTP limitations. Mark On Wed, Feb 10, 2016 at 5:59 AM Ragothaman Yennamalli wrote: > Hi Everyone, > > I am trying to install the latest version of Gromacs. Before, I mention the > real question I have to let you know that our system admin has diabled FTP > downloads. (Don't ask me why, but all FTP usages in the campus are banned) > So, thanks to a Chrome extension I was able to download the gromacs > installation package using the browser. > However, while installing I realized that Gromcas tried to download the > regression tests package via FTP and it was unable to the installation was > unsuccessful. I have downloaded the regressiontests package from the > browser and trying to install it again. > > So, my question is: Can I install Gromacs by bypassign FTP downloads? > > Thanks for any input! > > Raghu > -- > 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.
