Re: [gmx-users] RDF calculation from surface of protein
-surf flag is used with -ref flag. Provide the reference file in the -ref flag. On Thu, Feb 6, 2020 at 1:52 AM Pandya, Akash wrote: > Hi all, > > I am trying to calculate the RDF between the protein surface and the > centre of mass of my ligand and water molecules. Please find below the > command I used: > > gmx rdf -s proteinLIG.tpr -f proteinLIG.xtc -n index.ndx -o rdf.xvg -bin > 0.02 -cn number.xvg -surf mol -seltype mol_com > > > I get the following error: > > > > Inconsistency in user input: > -surf only works with -ref that consists of atoms > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > > I am wondering what this error means? My ref group does contain atoms? Any > guidance will be much appreciated :) > > > Akash > -- > 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. > -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- 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] RDF calculation from surface of protein
Hi all, I am trying to calculate the RDF between the protein surface and the centre of mass of my ligand and water molecules. Please find below the command I used: gmx rdf -s proteinLIG.tpr -f proteinLIG.xtc -n index.ndx -o rdf.xvg -bin 0.02 -cn number.xvg -surf mol -seltype mol_com I get the following error: Inconsistency in user input: -surf only works with -ref that consists of atoms For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I am wondering what this error means? My ref group does contain atoms? Any guidance will be much appreciated :) Akash -- 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] RDF calculation
Dear all, I have a curved rod-like micelle formed by three different molecules. I want to calculate the RDF of constituent molecules. I want to select the center line of the curved cylindir-like structure as a reference point. How can I do that? I am using Gromacs version 5.1.2. with Martini Force field. Any suggestions would be helpful. Many thanks, Esra -- 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] rdf calculation for wormlike micelles
Dear Joe, Sorry for the confusion. I am working with martini force field and I have three different molecules in the micelle structure. I want to analyze the RDF of the constituent molecules with respect to the line that pass through the center along with its length. As I mention before this line has a curved structure and I couldn’t figure out how to select that line as a reference point. I guess a picture would be more helpful to explain my purpose. It is similar to the Figure 3 in the paper that I gave the link below: https://pubs.acs.org/doi/10.1021/acs.langmuir.7b01176 Many thanks, Esra 2018-03-14 17:51 GMT+03:00 : > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. Re: gromacs.org_gmx-users Digest, Vol 167, Issue 73 (Esra ka?ar) >2. Re: gromacs.org_gmx-users Digest, Vol 167, Issue 73 (Joe Jordan) >3. Umbrella Sampling - good histogram but no result in profile > (Ben Tam) >4. Re: Umbrella Sampling - good histogram but no result in > profile (Mark Abraham) > > > -- > > Message: 1 > Date: Wed, 14 Mar 2018 16:28:19 +0300 > From: Esra ka?ar> To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue > 73 > Message-ID: >
Re: [gmx-users] rdf calculation for wormlike micelles
You cannot use a line as the reference. From a brief glance at the paper you link it seems like maybe you actually want to compute the expectation value of the micelle backbone, a method known as principle curves which is a generalization of principle component analysis. At any rate, you should probably just follow whatever procedure they use in the paper you are citing. On Thu, Mar 15, 2018 at 7:48 AM, Esra Kaçarwrote: > Dear Joe, > > Sorry for the confusion. I am working with martini force field and I have > three different molecules in the micelle structure. I want to analyze the > RDF of the constituent molecules with respect to the line that pass through > the center along with its length. As I mention before this line has a > curved structure and I couldn’t figure out how to select that line as a > reference point. I guess a picture would be more helpful to explain my > purpose. It is similar to the Figure 3 in the paper that I gave the link > below: > > https://pubs.acs.org/doi/10.1021/acs.langmuir.7b01176 > > Many thanks, > > Esra > -- > 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. -- Joe Jordan -- 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] rdf calculation for wormlike micelles
Dear Joe, Sorry for the confusion. I am working with martini force field and I have three different molecules in the micelle structure. I want to analyze the RDF of the constituent molecules with respect to the line that pass through the center along with its length. As I mention before this line has a curved structure and I couldn’t figure out how to select that line as a reference point. I guess a picture would be more helpful to explain my purpose. It is similar to the Figure 3 in the paper that I gave the link below: https://pubs.acs.org/doi/10.1021/acs.langmuir.7b01176 Many thanks, Esra -- 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] rdf calculation for wormlike micelles
See here for info on the selection syntax http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html On Wed, Mar 14, 2018 at 10:01 AM, Esra Kaçarwrote: > Dear all, > > I am working on a wormlike micelle that has a curved structure. I want to > calculate the radial distribution functions of constituent molecules with > respect to the backbone (the line following the micelle length and > represents the center of the curved cylindrical structure) of the wormlike > micelle. Since the structure is curved, I couldn’t find out how to select > the backbone as a reference point in g_rdf. I am using Gromacs v 5.1. Any > suggestions would be appreciated. > > Thanks, > > Esra > -- > 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. -- Joe Jordan -- 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] rdf calculation for wormlike micelles
Dear all, I am working on a wormlike micelle that has a curved structure. I want to calculate the radial distribution functions of constituent molecules with respect to the backbone (the line following the micelle length and represents the center of the curved cylindrical structure) of the wormlike micelle. Since the structure is curved, I couldn’t find out how to select the backbone as a reference point in g_rdf. I am using Gromacs v 5.1. Any suggestions would be appreciated. Thanks, Esra -- 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] RDF calculation
Dear gmx-users, I am new to Gromacs. I have a droplet including some types of lipids such as DPPC. I want to calculate RDF for head atom of DPPC with respect to droplet center-of-mass. My question is how can i calculate this issue in versions 2017. Apparently this feature has been removed from current version (5.1.x). Please help me. Thanks Farrokh -- 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] rdf calculation with respect to center of mass
Dear gmx-users, The radial distribution function with respect to center-of-mass was computable in old gromacs versions. How can I calculate that in newer version(2016)? Thanks in advance. Maryam -- 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] RDF calculation.
Hi, I am studying the dynamics of a double stranded DNA in presence of small molecules. I want to study the preferential binding of these molecules in the grooves and backbones of the DNA and also calculate the feasibility of these binding in terms of calculating the free energy change.My question is- 1. while calculating radial distribution functions say between DNA minor groove and choline, should I consider the center-off-mass atom of the minor groove by using the -COM option of g_rdf? 2. Do you think calculation of PMF from g(r) for a specific ion binding with the DNA can provide reliable free energy change or do I have to switch to umbrella sampling? PS: I only want to investigate the small molecule binding, not the stability of the DNA duplex as a whole. Thanks for your time in advance. Soumadwip Ghosh Research Fellow Indian Institute of Technology Bombay 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.
Re: [gmx-users] RDF calculation.
Well, since you are not interested in the duplex stability, I would not use -COM. See, during the simulation, the center-of-mass of such a small helix part can drastically move, leading to a questionable result. Check your system and make sure that you will not face this situation. About the PMF, that depends on the ions you are using and the forcefields. It is already known that some of them are poorly described, so check that out too. Hope it can help! Cheers! 2014-12-27 7:17 GMT-02:00 soumadwip ghosh soumadwipgh...@gmail.com: Hi, I am studying the dynamics of a double stranded DNA in presence of small molecules. I want to study the preferential binding of these molecules in the grooves and backbones of the DNA and also calculate the feasibility of these binding in terms of calculating the free energy change.My question is- 1. while calculating radial distribution functions say between DNA minor groove and choline, should I consider the center-off-mass atom of the minor groove by using the -COM option of g_rdf? 2. Do you think calculation of PMF from g(r) for a specific ion binding with the DNA can provide reliable free energy change or do I have to switch to umbrella sampling? PS: I only want to investigate the small molecule binding, not the stability of the DNA duplex as a whole. Thanks for your time in advance. Soumadwip Ghosh Research Fellow Indian Institute of Technology Bombay 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. -- Marcelo Depólo Polêto Biochemicist University of Viçosa - Brazil -- 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] RDF calculation.
On 12/27/14 4:17 AM, soumadwip ghosh wrote: Hi, I am studying the dynamics of a double stranded DNA in presence of small molecules. I want to study the preferential binding of these molecules in the grooves and backbones of the DNA and also calculate the feasibility of these binding in terms of calculating the free energy change.My question is- 1. while calculating radial distribution functions say between DNA minor groove and choline, should I consider the center-off-mass atom of the minor groove by using the -COM option of g_rdf? I'm not sure it's useful. Choline is a rather flexible molecule, so simply considering the COM of the minor groove vs. all atoms of choline is probably going to give you a very noisy profile. 2. Do you think calculation of PMF from g(r) for a specific ion binding with the DNA can provide reliable free energy change or do I have to switch to umbrella sampling? This doesn't generally work well for ions, but the quality depends on the force field. Depending on what the ion is, the exchange rate may be impossible to observe in an atomistic simulation. The exchange rates for most common ions can range from nanosecond (feasible with MD) to microsecond (not reasonable, even if the force field is very accurate). -Justin PS: I only want to investigate the small molecule binding, not the stability of the DNA duplex as a whole. Thanks for your time in advance. Soumadwip Ghosh Research Fellow Indian Institute of Technology Bombay India -- == 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.