Re: [gmx-users] Choosing Parameter values of PTMs
You can have a look at few related work: http://selene.princeton.edu/FFPTM/ http://vienna-ptm.univie.ac.at/ http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003154 -- Thanks and Regards, Bipin Singh On Thu, Feb 11, 2016 at 6:29 PM, David Newman < david.newma...@postgrad.manchester.ac.uk> wrote: > Hi all, > > I'm starting a MD project using gromacs and we're looking to expand on the > previous work in the lab modelling our receptors of interest by looking at > the effects of gylcosylation. Is there a current best standard for > parameters for modelling glycans? > > 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. > -- 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 make .trr file readable
http://pythonhosted.org/MDAnalysis/documentation_pages/coordinates/TRR.html -- Thanks and Regards, Bipin Singh On Tue, Dec 1, 2015 at 6:10 PM, Ayesha Kanwal wrote: > Dear Gromacs experts, > i am very new to Gromacs i only want to take .trr file and make it > readable . as i want to use .trr file in my own tool as an input format. > how can i make it readable and can use it in my tool ? > Best regards > Ayesha > > -- > 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] Cross-correlation map of protein residues
There is a modified version of g_covar available at the below link for calculating correlation matrix: http://www.gromacs.org/Downloads/User_contributions/Other_software http://www.gromacs.org/@api/deki/files/55/=g_covar.tgz -- Thanks and Regards, Bipin Singh On Fri, Jul 17, 2015 at 6:51 PM, Ebert Maximilian wrote: > Dear list, > > I am looking for a gromacs tool which is able to calculate/draw a map of > residues which are either in their motion correlated or anti correlated. > first i thought i could just use g_covar with c-alpha and use the -xpma > option but while reading previous mailing list posts people said that the > atomic covariance matrix does not correlate motions. All posts I found > where older and the script from the gromacs site for a g_covar tool which > can calculate the correlation plot is from 2009. Therefore, i wanted to > know if gromacs 5 is able to directly calculate the plot. if not does > anybody know a straight forward way of doing so for a gromacs trajectory? > > thank you very much, > > max > -- > 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] Free energy change with harmonic restraints
I think It means that, you can use "restraint-lambdas" as a vector to control the restraints (bond, angle dihedral) while using the pull-code and get the corresponding free energy change (I suppose). -- Thanks and Regards, Bipin Singh On Fri, Jul 10, 2015 at 12:39 AM, Natalie Nguyen wrote: > Dear Asaf, > > Thank you again for putting in the time to respond to me so quickly. > What I have been trying to do was start from a system that is not > restrained and grow the restraints onto the ligand, measuring the change in > free energy of this. The harmonic restraints used are that of the umbrella > pull code with a force constant of k= 1000 kJ/mol*nm^2. It is mentioned In > the Gromacs manual for mdp options that the pull code can be controlled > with "restraint-lambdas", but there is not much detail other than this. I > imagine that lambda =0 would represent a nonexistent potential with k= 0 > and at lambda = 1 a full strength potential would be imposed. > Please feel free to ask me to add more detail! > > Warm regards, > Natalie > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > asaffa...@post.tau.ac.il > Sent: Thursday, July 09, 2015 10:38 AM > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Free energy change with harmonic restraints > > Dear Natalie, > > You are welcome. > Could you please explain in more detail so maybe I can help? > Do you want to change the strength of the restraints and measure the > free energy difference associated with this change? > > Thanks. p.s there is also http://arxiv.org/pdf/1307.1620v7.pdf with > the same equations. > > Best regards, > Asaf > > Quoting Natalie Nguyen : > > > Dear Asaf, > > > > Thank you for the quick reply! > > > > I was wondering if it was possible to use thermodynamic integration > > to represent growing harmonic restraints aside from using an > > analytical method. > > > > I will cite this article most definitely! > > > > Natalie Nguyen > > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > > on behalf of > > asaffa...@post.tau.ac.il > > Sent: Thursday, July 09, 2015 7:45 AM > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: Re: [gmx-users] Free energy change with harmonic restraints > > > > Dear Natalie, > > > > You have in > > > > http://xxx.tau.ac.il/pdf/1502.07196v3.pdf > > > > exact free energy of harmonic covalent bond and bond angle terms (or > > restrains). See Eqs. (2) and (3). > > > > There are also previous studies in the references there. > > > > For the dihedral term I assume it can also be calculated exactly (I > > might upload it). > > > > There is also to think if there are other contributions. > > > > If you are using it please cite. > > > > Best regards, > > Asaf > > > > > > Quoting Natalie Nguyen : > > > >> Dear all, > >> > >> > >> I am trying to measure the free energy change associated with > >> adding/removing harmonic restraints imposed on a ligand that is > >> attached to a protein. Is there any way to set this up? > >> > >> > >> Thank you ahead of time! > >> > >> > >> Natalie Nguyen > >> -- > >> 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
Re: [gmx-users] Regarding difference in SASA values using GMX versions 5.X and 4.X
Thanks Mark for your comments. -- Thanks and Regards, Bipin Singh On Thu, May 28, 2015 at 9:05 PM, Mark Abraham wrote: > Hi, > > On Thu, May 28, 2015 at 5:23 PM bipin singh wrote: > > > Hi all, > > > > I have calculated SASA for a group amino acid residues using GMX versions > > 5.0.1 and 4.6.3 and noted that there is significant difference in the > > calculated values, as can be seen in figure at the link below. > > > > > > > https://drive.google.com/file/d/0ByHdYJNF-aRrTEFtNDR5dEEyZlU/view?usp=sharing > > > > I know that it is already mentioned that from version 5.0 GMX uses the > Van > > der Waals radii from paper "A. Bondi, van der Waals Volumes and Radii, J. > > Phys. Chem. 68 (1964) pp. 441-451", and it is expected to be different > > compared to previous GMX versions. However I wanted to know what was the > > source of Van der Waals radii in GMX 4.X versions > > > History is silent, so probably someone made stuff up in a vaguely plausible > manner. > > and which one is > > considered to be more accurate. > > > > "Accurate" depends on the purpose, and requires someone to show that > certain radii correlate best with whatever other quantities. (How big is an > electron cloud, anyway?) For observing qualitative differences in solvent > accessibility of two configurations, probably any guess is as good as > another... > > Mark > > > > > > -- > > Thanks and Regards, > > Bipin Singh > > -- > > 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.
[gmx-users] Regarding difference in SASA values using GMX versions 5.X and 4.X
Hi all, I have calculated SASA for a group amino acid residues using GMX versions 5.0.1 and 4.6.3 and noted that there is significant difference in the calculated values, as can be seen in figure at the link below. https://drive.google.com/file/d/0ByHdYJNF-aRrTEFtNDR5dEEyZlU/view?usp=sharing I know that it is already mentioned that from version 5.0 GMX uses the Van der Waals radii from paper "A. Bondi, van der Waals Volumes and Radii, J. Phys. Chem. 68 (1964) pp. 441-451", and it is expected to be different compared to previous GMX versions. However I wanted to know what was the source of Van der Waals radii in GMX 4.X versions and which one is considered to be more accurate. -- Thanks and Regards, Bipin Singh -- 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] Doubt regarding nrexcl parameter in topology
Thank you Chandan for your reply and explanation. -- Thanks and Regards, Bipin Singh On Sat, Jan 17, 2015 at 11:53 AM, Chandan Choudhury wrote: > Dear Bipin, > > With nrexcl = 3 it excludes neighbours 3 bonds away, in this case your (ii) > option falls. > But an extra LJ and electrostatic interactions, is added between 1-4 pairs, > if gen-pair is yes for the force field. > These interactions are scaled by their respective fudge factor. > For gromos ff, the gen-pair is no. Thus there are no extra LJ or > electrostatics. 1-4 pair contributes to the potential energy > only through dihedrals. > > Chandan > > > On Sat, Jan 17, 2015 at 7:42 AM, bipin singh wrote: > > > Dear All, > > > > I have a doubt regarding the definition of nrexcl parameter in topology > of > > a molecule (Gromos force field) > > > > > > As mebtioned in the Gromacs manual, nrexcl = 3 stands for excluding > > non-bonded interactions between atoms that are no further than 3 bonds > > away, so does it mean that: > > > > > > (i) Exclude the 1-2 and 1-3 pairs and but not the 1-4 pair. > > > > OR > > > > (ii) Exclude the 1-2, 1-3 and the 1-4 pairs. > > > > > > Thanks and Regards > > Bipin > > -- > > 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. > > > > > > -- > > -- > Chandan Kumar Choudhury > National Chemical Laboratory, Pune > India > > *"All work and no play makes Jack a dull boy...”* > -- > 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] Doubt regarding nrexcl parameter in topology
Dear All, I have a doubt regarding the definition of nrexcl parameter in topology of a molecule (Gromos force field) As mebtioned in the Gromacs manual, nrexcl = 3 stands for excluding non-bonded interactions between atoms that are no further than 3 bonds away, so does it mean that: (i) Exclude the 1-2 and 1-3 pairs and but not the 1-4 pair. OR (ii) Exclude the 1-2, 1-3 and the 1-4 pairs. Thanks and Regards Bipin -- 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] AMBER99 topology for ADP
http://www.pharmacy.manchester.ac.uk/bryce/amber/ -- Thanks and Regards, Bipin Singh On Thu, Jan 15, 2015 at 7:48 PM, Marc Hoemberger wrote: > Hello, > > Does someone have the topology file of ADP for the AMBER forcefield? > > Best regards, > Marc Hoemberger > > -- > 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] Dihedral pca
I don't think the definition of omega dihedral which you have written is correct, -- Thanks and Regards, Bipin Singh On Sat, Jan 3, 2015 at 12:22 AM, pratibha kapoor wrote: > Hi, > > Please correct me if I am wrong but I believe that since torsion angle > omega is defined by 4 points in space namely Calpha (n) ,carbonyl carbon, > nitrogen, and calpha (n+1), omiting or including carbonyl oxygen (i.e. > using mainchain or backbone options) would not make a difference. > Secondly, is it reasonable enough to exclude carbonyl oxygen atoms while > calculating dihedral angles? > I apologize beforehand for the ignorance. > > Waiting for reply. > Thanks > > On Fri, Jan 2, 2015 at 7:36 PM, pratibha kapoor > > wrote: > > > Hi Bipin > > > > Thanks for the reply. > > I have a small doubt won't selecting mainchain would also give owega > > rather than only phi-psi angles? > > > > Thanks > > > > On Fri, Jan 2, 2015 at 6:14 PM, pratibha kapoor < > kapoorpratib...@gmail.com > > > wrote: > > > >> Hi, > >> > >> I would like to carry out dihedral pca with the dihedral angles (phi and > >> psi) of the peptide backbone. My question is how should I select my > >> dihedral angles? > >> I am using > >> mk_angndx -s *.tpr -n angle.ndx > >> The angle.ndx file so created contains all the dihedral angles I guess. > >> How should I select only the phi, psi dihedrals of peptide backbone? > >> Also, I am not able to understand the meaning of > >> [ Phi=180.0_2_33.50 ] > >> etc. terms in the index file. > >> Please guide me in proceeding further. > >> > >> 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. > -- 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] Dihedral pca
Yes, may be it will include omega too, but I am not sure. In that case, you may select only the backbone atoms. -- Thanks and Regards, Bipin Singh On Fri, Jan 2, 2015 at 7:36 PM, pratibha kapoor wrote: > Hi Bipin > > Thanks for the reply. > I have a small doubt won't selecting mainchain would also give owega rather > than only phi-psi angles? > > Thanks > > On Fri, Jan 2, 2015 at 6:14 PM, pratibha kapoor > > wrote: > > > Hi, > > > > I would like to carry out dihedral pca with the dihedral angles (phi and > > psi) of the peptide backbone. My question is how should I select my > > dihedral angles? > > I am using > > mk_angndx -s *.tpr -n angle.ndx > > The angle.ndx file so created contains all the dihedral angles I guess. > > How should I select only the phi, psi dihedrals of peptide backbone? > > Also, I am not able to understand the meaning of > > [ Phi=180.0_2_33.50 ] > > etc. terms in the index file. > > Please guide me in proceeding further. > > > > 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. > -- 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] Dihedral pca
For extracting all the atoms involved in the phi-psi dihedral, you can use make_ndx and select Mainchain group, then you can extract all the dihedrals from the trajectory using the below command: g_angle -f foo.xtc -s foo.tpr -n dangle.ndx -or dangle.trr -type dihedral As described here: http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA -- Thanks and Regards, Bipin Singh On Fri, Jan 2, 2015 at 6:14 PM, pratibha kapoor wrote: > Hi, > > I would like to carry out dihedral pca with the dihedral angles (phi and > psi) of the peptide backbone. My question is how should I select my > dihedral angles? > I am using > mk_angndx -s *.tpr -n angle.ndx > The angle.ndx file so created contains all the dihedral angles I guess. How > should I select only the phi, psi dihedrals of peptide backbone? > Also, I am not able to understand the meaning of > [ Phi=180.0_2_33.50 ] > etc. terms in the index file. > Please guide me in proceeding further. > > 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. > -- 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] Fatal error during entropy calculation using g_anaeig
Hi all, I am trying to calculate entropy using g_anaeig (Gromacs version 5.0.1), after using g_nmeig to calculate eigenvectors and eigenvalues (after computing hessian matrix): g_nmeig_mpi -f hessian.mtx -s run.tpr -nom g_anaeig_mpi -v eigenvec.trr -entropy But I am getting the following error: Fatal error: Can not calculate entropies from mass-weighted eigenvalues, redo the analysis without mass-weighting. -- Thanks and Regards, Bipin Singh -- 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] Error during entropy calculation
Hi all, I am trying to calculate entropy using g_anaeig (Gromacs version 5.0.1), after using g_nmeig to calculate eigenvectors and eigenvalues (after computing hessian matrix): g_nmeig_mpi -f hessian.mtx -s run.tpr -nom g_anaeig_mpi -v eigenvec.trr -entropy But I am getting the following error: Fatal error: Can not calculate entropies from mass-weighted eigenvalues, redo the analysis without mass-weighting. -- Thanks and Regards, Bipin Singh -- 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] Regarding Null free energy values in Free energy perturbation (bond force constant perturbation)
Hi all, I am trying to perform a free energy perturbation calculation (using Gromacs 4.6.3) to perturb the force constant of a bond (in vaccum), using the B-state parameters in the topology as follows: [ bonds ] ; ai aj funct c0 c1c0B c1B 342 0.1090 1.2300e+07 0.1090 6.1500e+08 I have used 20 intermediate states between lambda=0 and 1. The MDP setting (only some part shown) used for the calculation are as follows: cutoff-scheme= group coulombtype = cut-off rcoulomb = 0.0 vdw-type = cut-off rvdw = 0.0 pbc = no nstlist = 0 ns-type = simple free-energy = yes couple-moltype = LIG sc-power = 1 sc-alpha = 0.0 sc-r-power = 6 sc-sigma = 0.3 sc-coul = no couple-intramol = yes couple-lambda1 = vdw-q ; Do not change the non-bonded int. during FEP couple-lambda0 = vdw-q init-lambda = 0.0 (set accordingly for other intermediates) delta-lambda = 0 foreign-lambda = 0.05 (set accordingly for other intermediates) nstdhdl = 10 dhdl-print-energy= no But the final DG values with g_bar gives null values as shown below: Final results in kJ/mol: point 0.000 - 0.050, DG 0.00 +/- 0.00 point 0.050 - 0.100, DG 0.00 +/- 0.00 point 0.100 - 0.150, DG 0.00 +/- 0.00 point 0.150 - 0.200, DG 0.00 +/- 0.00 point 0.200 - 0.250, DG 0.00 +/- 0.00 point 0.250 - 0.300, DG 0.00 +/- 0.00 point 0.300 - 0.350, DG 0.00 +/- 0.00 point 0.350 - 0.400, DG 0.00 +/- 0.00 point 0.400 - 0.450, DG 0.00 +/- 0.00 point 0.450 - 0.500, DG 0.00 +/- 0.00 point 0.500 - 0.550, DG 0.00 +/- 0.00 point 0.550 - 0.600, DG 0.00 +/- 0.00 point 0.600 - 0.650, DG 0.00 +/- 0.00 point 0.650 - 0.700, DG 0.00 +/- 0.00 point 0.700 - 0.750, DG 0.00 +/- 0.00 point 0.750 - 0.800, DG 0.00 +/- 0.00 point 0.800 - 0.850, DG 0.00 +/- 0.00 point 0.850 - 0.900, DG 0.00 +/- 0.00 point 0.900 - 0.950, DG 0.00 +/- 0.00 point 0.950 - 1.000, DG 0.00 +/- 0.00 total 0.000 - 1.000, DG 0.00 +/- 0.00 Please let me know, what could be the reason for this behavior. *---Thanks and Regards,Bipin Singh* -- 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] How to change the multiplicity of a dihedral in FEP in Gromacs
Hi all, I want to change the multiplicity of a dihedral, using the B-state topology in FEP calculations using Gromacs. As shown below: [ dihedrals ] ; ai aj ak al functph0 cp mult ph0B cpB multB 32561 0.00 5.923 180 1.00 6 I know, that the multiplicity can not be altered in FEP calculation in Gromacs, but is there any way to achieve the above transformation by some other means. -- Thanks and Regards, Bipin Singh -- 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] Regarding the generation of intermolecule disulphide bond between two monomer subunits
Thank you Dr. Justin for your reply. I am able to solve the problem by using the -chainsep and -merge option simultaneously. *---Thanks and Regards,Bipin Singh* On Wed, Dec 10, 2014 at 6:15 PM, Justin Lemkul wrote: > > > On 12/10/14 7:29 AM, bipin singh wrote: > >> Hi all, >> >> I want to generate a disulphide bond between two cysteine residues of two >> monomers of a protein, to create a dimer protein. But, it is not happening >> while running the pdb2gmx, because there is TER record at the end of one >> monomer subunit pdb file. However, using the -chainsep option and defining >> the two monomers as a single molecule generate the disulphide bond but >> cause the formation of peptide bond between the two terminal ends of >> monomer chains. >> Please let me know, if there is any other way to make intermolecule >> disulphide bond, without linking the two monomers ends with peptide bond. >> >> > Proper use of -chainsep and -merge is all it takes to get this to work, > but you haven't shown us what you've actually done. Provide exact commands > and relevant output, and we can suggest something. But this can certainly > be done with those two options. > > -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] Regarding the generation of intermolecule disulphide bond between two monomer subunits
Hi all, I want to generate a disulphide bond between two cysteine residues of two monomers of a protein, to create a dimer protein. But, it is not happening while running the pdb2gmx, because there is TER record at the end of one monomer subunit pdb file. However, using the -chainsep option and defining the two monomers as a single molecule generate the disulphide bond but cause the formation of peptide bond between the two terminal ends of monomer chains. Please let me know, if there is any other way to make intermolecule disulphide bond, without linking the two monomers ends with peptide bond. *---Thanks and Regards,Bipin Singh* -- 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] Question about n-linked glycans
Hope this help. http://glycam.org/ Thanks and Regards, Bipin Singh On Sun, Sep 28, 2014 at 8:45 AM, Mikhail Yustanov wrote: > Hi all, > > I am trying to study the influences of N linked glycans on protein > stability. I am very new to MD Simulations. I wonder what is the best way > to generate a topology file for the glycoprotein. Is there AMBER/GLYCAM > integrated force field presently available? I have read through the basic > and membrane tutorial but am still lost. > > Thank you, > > Mikhail > > Sent from my iPod > -- > 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] (no subject)
something wrong with the input atom index. Thanks and Regards, Bipin Singh On Fri, Sep 12, 2014 at 3:44 PM, Namita Singh wrote: > i want to generate a log file for residue residue contact of a > protein-protein complex.I am using > > g_hbond -s a.tpr -f c.xtc -r 0.55 -num hbond.xvg -g hbond.log -n > atom_index.ndx -contact > bt i am not getting any log file. > -- > 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] DSSP
check the permissions of dssp executables and give the execute permission if it is not already. *Thanks and Regards,Bipin Singh* On Mon, Aug 25, 2014 at 6:26 PM, Nikolaos Michelarakis wrote: > Yes, this is the command i am using: > > do_dssp -s npt-nopr.tpr -f npt-nopr.trr -o fws-ss.xpm -ver 2 > > whether i include -ver 2 or not makes no difference, I still get the same > error. > > Cheers, > > Nicholas > > > On 25 August 2014 15:53, Mark Abraham wrote: > > > Have you read and followed gmx do_dssp -h? > > > > Mark > > > > > > On Mon, Aug 25, 2014 at 2:21 PM, Nikolaos Michelarakis > > > wrote: > > > > > Hello, > > > > > > Thank you all for your help! I got it working by downloading the > > > executables directly and setting the path but i do get the > > > > > > Program do_dssp, VERSION 5.0 > > > Source code file: > > > > > > > > > /home/jslatter/programs/gromacs/gromacs-5.0/src/gromacs/gmxana/gmx_do_dssp.c, > > > line: 670 > > > > > > Fatal error: > > > Failed to execute command: Try specifying your dssp version with the > -ver > > > option. > > > > > > error. No matter which version i specify, it persists, any ideas? > > > > > > Cheers, > > > > > > Nicholas > > > -- > > > 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] DSSP
You may download the relevant executables from the following links: ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386 ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-win32.exe before using the do_dssp module of Gromacs, export the path to the above executable dssp as: export dssp=/path/to/dssp/executable then run the do_dssp as usual. *Thanks and Regards,Bipin Singh* On Mon, Aug 25, 2014 at 7:38 AM, Nikolaos Michelarakis wrote: > Hi, > > Thank you for your answer, could you please give me some more info on where > to find them and how to use them for the whole trajectory? > > Cheers, > > Nicholas > -- > 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] DSSP
You may use the precompiled dssp executables. *Thanks and Regards,Bipin Singh* On Mon, Aug 25, 2014 at 5:31 AM, Nikolaos Michelarakis wrote: > Hello, > > I am trying to do a secondary structure analysis to get the percentages of > each secondary structure in my protein. I know i can use do_dssp but > unfortunately DSSP is not installed on the cluster that i have been using > and i do not have the acess to install it. Any other ways to do it? or > would anyone be able to run it for me? I need it for 3 structures, for 3 > different forcefields, 9 structures overall. > > Thanks a lot, > > Nicholas > -- > 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] Forcefield parameters for Zinc and phosphorylated residues
This might help. http://vienna-ptm.univie.ac.at/ *Thanks and Regards,Bipin Singh* On Wed, Aug 20, 2014 at 4:30 PM, Michael Carter wrote: > Hi, > > I have two questions regarding the parameterisation of Zinc ions and a > phosphorylated TYR residue within two different protein systems. > > > 1. Zinc parameters: > > I have three zinc ions within one protein system. I want to use a bonded > model so that they do not fly out of my protein upon simulation. Is there > any documentation on the parameters for such a model in the GROMOS > forcefield? > > 2. Phosphorylated TYR > > In another system I have a phosphorylated TYR residue. PDB2GMX does not > like this and after looking inot the manual I have found that you can add > parameters for this to the existing forcefields. Much like the previous > question, is there any documentation on the addition of parameters for > phosphorylated residues in the GROMOS forcefield? > > Any pointers for these questions would be greatly appreciated. > > Cheers, > Mike Carter > > The Institute of Cancer Research: Royal Cancer Hospital, a charitable > Company Limited by Guarantee, Registered in England under Company No. > 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. > > This e-mail message is confidential and for use by the addressee only. If > the message is received by anyone other than the addressee, please return > the message to the sender by replying to it and then delete the message > from your computer and network. > -- > 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] Regarding the difference between g_dipoles and g_dielectric calculations
Hi All, Can someone give me some insights regarding the context under which we use the g_dipoles or g_dielectric (as mentioned below the two possible way of calculating dielectric constant) to calculate the dielectric constant of some molecule during simulation. g_dipoles computes the total dipole plus fluctuations of a simulation system. >From this you can compute e.g. the dielectric constant for low-dielectric media. g_dielectric calculates frequency dependent dielectric constants from the autocorrelation function of the total dipole moment. Thanks and Regards, Bipin Singh -- 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] Calculating dielectric constant using g_dipoles and g_dielectric
Hi All, Can someone give me some insights regarding the context under which we use the g_dipoles or g_dielectric (as mentioned below the two possible way of calculating dielectric constant) to calculate the dielectric constant of some molecule during simulation. g_dipoles computes the total dipole plus fluctuations of a simulation system. >From this you can compute e.g. the dielectric constant for low-dielectric media. g_dielectric calculates frequency dependent dielectric constants from the autocorrelation function of the total dipole moment. Thanks and Regards, Bipin Singh -- 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 Ligand Interaction or Docking using Gromacs
A reference: http://pubs.acs.org/doi/abs/10.1021/jz301635h On Wed, Apr 23, 2014 at 1:54 PM, andrea wrote: > Brute force is one solution (long simulation). > You can have look to "accelerated MD" or "rare event MD" in pubmed. You > will find that docking a ligand onto the receptor by MD is feasible using > new strategies based (i.e. metadynamics with plumed plugin in gromacs) > > cheers > > and > > > On 23/04/2014 10:14, ms wrote: > >> On 4/23/14 9:55 AM, neha_bharty wrote: >> >>> Hello >>> >>> I want to find the protein ligand interaction using gromacs. >>> Is it possible to perform protein-ligand docking with the help of >>> gromacs or >>> I have to dock the protein and ligand with some tools like autodock and >>> then >>> only I can view its interaction using gromacs?? >>> >> In theory it is possible to put the ligand in solution and wait for it to >> attach to the protein, in a molecular dynamics simulation. However in >> practice this is almost impossible unless you are going to do very, *very* >> huge simulations. The group of David Shaw did that with his custom Anton >> hardware (and Desmond, not Gromacs): http://www.pnas.org/content/ >> 108/32/13118.long >> >> So, the *practical* answer would be: yes, usually you need to dock the >> ligand first in some reasonable binding pose. You can use "classical" >> Autodock, VINA/Idock or even better HADDOCK to do that. >> >> >>> Is there any tutorial to perform Protein - ligand interaction or docking >>> using gromacs?? >>> >> Google is your friend. http://www.bevanlab.biochem. >> vt.edu/Pages/Personal/justin/gmx-tutorials/complex/ >> >> which force field or time steps are require for this study? >>> >> A force field compatible with the way you parametrized your ligand, I >> would say. The tutorial linked above covers this issue. >> >> Massimo >> >> Thanks. >>> >>> -- >>> View this message in context: http://gromacs.5086.x6.nabble. >>> com/Re-Protein-Ligand-Interaction-or-Docking-using- >>> Gromacs-tp5016011.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. > -- === Thanks and Regards, Bipin Singh Ph.D. Student in Bioinformatics CCNSB, IIIT-Hyderabad bipin.si...@research.iiit.ac.in http://researchweb.iiit.ac.in/~bipin.singh === -- 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] the result of the free energy
First you should go through the literature related to free energy calculations: http://www.alchemistry.org/wiki/Intermediate_States http://www.ncbi.nlm.nih.gov/pubmed/23034753 On Thu, Apr 10, 2014 at 8:10 PM, jane <348363...@qq.com> wrote: > Hi all, > when i calculate the free energy of a molecule, the result is as the > picture > . i do not understand the true meaning. what is the relationship between > dH/d(lambda) the .xvg file got and the free energy ? and what is the > meaning > of the lambda ? thank you in advance. > <http://gromacs.5086.x6.nabble.com/file/n5015785/Screenshot-2.png> > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/the-result-of-the-free-energy-tp5015785.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.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. > -- Thanks and Regards, Bipin Singh CCNSB, IIIT-H <http://researchweb.iiit.ac.in/~bipin.singh> -- 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] Error in g_bar
Hi all,
I am getting the following error while running g_bar:
Program g_bar_mpi, VERSION 4.6.5
Source code file: /sw/source/sandbox/gromacs-4.6.5/src/tools/gmx_bar.c,
line: 1204
Fatal error:
Could not find a set for foreign lambda = 0.00
in the files for lambda = 0.00
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
I think this is similar to what Prof. David has posted (below) some days
back.
##
Hi,
I have a problem with g_bar in 4.6.5
Program g_bar, VERSION 4.6.5
Source code file: /afs/
hpc2n.umu.se/lap/gromacs/4.6.5/src/gromacs-4.6.5/src/tools/gmx_bar.c, line:
1204
Fatal error:
Could not find a set for foreign lambda = 0.00
in the files for lambda = 0.00
We have
lambda_0.00.xvg:
@ s0 legend "dH/d\xl\f{} fep-lambda = 0."
@ s1 legend "\xD\f{}H \xl\f{} to 0."
@ s2 legend "\xD\f{}H \xl\f{} to 0.0250"
lambda_0.025.xvg:
@ s0 legend "dH/d\xl\f{} fep-lambda = 0.0250"
@ s1 legend "\xD\f{}H \xl\f{} to 0."
@ s2 legend "\xD\f{}H \xl\f{} to 0.0250"
@ s3 legend "\xD\f{}H \xl\f{} to 0.0500"
lambda_0.05.xvg
@ s0 legend "dH/d\xl\f{} fep-lambda = 0.0500"
@ s1 legend "\xD\f{}H \xl\f{} to 0.0250"
@ s2 legend "\xD\f{}H \xl\f{} to 0.0500"
And so on.
Any clue?
######
--
Thanks and Regards,
Bipin Singh
CCNSB, IIIT-H <http://researchweb.iiit.ac.in/~bipin.singh>
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Re: [gmx-users] Regarding 1-d free energy profile from g_sham
Hi Richa, I was not able to get exactly what I wanted. As you know the g_sham output does not give you the energy Vs PC information, rather it gives energy Vs bin index information. So, the problem is how to transform bin index information into PC values. As I was not much interested in exact PC values, so I have tried to find out the PC values where the system spends most of the time (from the PC Vs time plot), once we find those PC values, then one can approximately map minimas in 1-d FEL to the corresponding approximate range of PC values. Again I will say this not the most accurate way of getting PC Vs energy information. For getting exact information there is no way to get it directly from g_sham without post processing its output as suggested by Dr. Justin. On Fri, Apr 4, 2014 at 5:43 PM, richa wrote: > Hi Bipin, > > Just went through your post. I also have the similar issue of making 1 D > free energy plots. I tried it with g_sham and got a file which contains the > bin index and 3 more columns. But I want the energies as a function of the > principal component I'm using. > > Could you please help me if you were able to plot the 1 D free energy > surfaces? > > thanks and regards > Richa > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Regarding-1-d-free-energy-profile-from-g-sham-tp4455745p5015645.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.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. > -- *Thanks and Regards, Bipin Singh* -- 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] about gromacs
http://manual.gromacs.org/online.html http://manual.gromacs.org/online/flow.html On Tue, Apr 1, 2014 at 9:53 AM, Meenakshi Rajput wrote: > hi..i have installed rpm version of gromacs on my machine with core i3 > processor. Can you send me the command list of gromacs. > -- > 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. > -- *Thanks and Regards,Bipin Singh* -- 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] help regarding building topology of Lanitibiotics (small natural peptides)
You may follow the following article for some help: http://pubs.acs.org/doi/abs/10.1021/sb400168u On Fri, Mar 28, 2014 at 7:16 PM, chetan kumar meena < chetan.shadowkillerme...@gmail.com> wrote: > try prodrug for small molecule for topology generation. > > > On Fri, Mar 28, 2014 at 3:03 PM, Gaurav Saraf IDD M Tech Biochem. Engg, IIT > (BHU) wrote: > > > Respected Sir/Ma'am > > > > I am new to the field of simulations and want to perform > > protein-peptide simulations. I am facing troubles with building the > > topology for my peptides as they contain various modified amino acids > > which the rtp does not recognise. > > > > Attachments: one of the pdb file of a lantibiotic (2KTO is the RCSB code) > > > > Thanking you, > > > > > > Yours sincerely, > > Gaurav > > School of Biochemical Engineering. > > Indian Insitute of Technology (BHU), Varanasi. > > 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. > > > > > > > -- > Regards > Chetan Kumar Meena > Ph.D. Bioinformatics > Pondicherry University > R28448 > PUDUCHERRY > Pin:605014 > -- > 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. > -- *Thanks and Regards,Bipin Singh* -- 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] Dihedral force constants
You can look at following reference for some common dihedral force constants: http://compbio.biosci.uq.edu.au/mediawiki/upload/3/36/Gromos53a5a6.pdf For dihedrals the units are in kj/mol not in kcal/mol/rad^2 (except impropers), also you have to convert kj to kcal. On Thu, Feb 20, 2014 at 9:44 AM, Dr. Ayan Datta wrote: > I was trying to find the dihedral force > constants for few typical bonds like C-C-C-C or C-C-C-N etc. (linear) etc. > in kcal/mol/deg^2 or kcal/mol/rad^2. > > Do you know a quick reference where few of these values are reported for > typical systems. > > Also, are the dihedral force constants known for some Silicon - Carbon > bonds. > > regards > Ayan > > > -- > Dr. Ayan Datta > Assistant Professor > Department of Spectroscopy > Indian Association for the Cultivation of Science > 2A & 2B Raja Subodh Mallick Road > Jadavpur, Kolkata - 700032 > West Bengal, 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. > -- *Thanks and Regards,Bipin Singh* -- 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 LJ energies during Free energy perturbation
Thank you Dr. Justin for your reply. On Sat, Feb 8, 2014 at 3:12 AM, Justin Lemkul wrote: > > > On 2/7/14, 9:13 AM, bipin singh wrote: > >> Hello All, >> >> Using a B state topology in mdp file, I have switched off the vdw and >> coulombic terms of a single atom in a molecule (H atom in CH3OH). I have >> tried to see how the LJ energies (between CH3OH and solvent) changes >> during >> the transformation (from lambda=0 to lambda=1) but I get zero values at >> both the lambda point (0 and 1) for both the LJ-SR and LJ-14 terms for >> CH3OH and solvent LJ interaction. >> >> > H atoms do not have LJ parameters in most force fields, so you will not > see any changes. LJ-14 are intramolecular and those interactions are going > to all be excluded anyway in CH3OH, but again if an H is changing, there > will be no difference in LJ energy. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > 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. > -- *Thanks and Regards,Bipin Singh* -- 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 LJ energies during Free energy perturbation
Hello All, Using a B state topology in mdp file, I have switched off the vdw and coulombic terms of a single atom in a molecule (H atom in CH3OH). I have tried to see how the LJ energies (between CH3OH and solvent) changes during the transformation (from lambda=0 to lambda=1) but I get zero values at both the lambda point (0 and 1) for both the LJ-SR and LJ-14 terms for CH3OH and solvent LJ interaction. I have used PME and cut-off for coulomb and vdw respectively in my mdp file. -- * Thanks and Regards,Bipin Singh* -- 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] Regarding Free energy perturbation
When we convert some atoms to a dummy atom (DUM) in a B state topology, then does the Gromacs free energy code automatically take care of this transformation in bonded terms (bond, angle, dihedral etc.) because we can not define B state parameters corresponding to bonded terms of dummy atoms in a topology. Another doubt is what would be the option need to be set in mdp file for " *couple-lambda1*" when we do free energy perturbation through B state topology: For example: At lambda=0, I have to use: couple-lambda0=vdw-q (all interactions are on at lambda=0 ) At lambda=1.0, I am not sure what should be the correct option: couple-lambda1=none; I think "none" option will not work here since I am selectively turning off vdw and charges for few atoms by changing it to dummy atom in B state topology. -- *----Thanks and Regards,Bipin Singh* -- 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] Regarding DUM atom in Gromos force field
Thanks Dr. Mark for your reply. My doubt is when we convert some atoms to a dummy atom (DUM) in a B state topology, then does the Gromacs free energy code automatically take care of this transformation in bonded terms (bond, angle, dihedral etc.) because we can not define B state parameters corresponding to bonded terms of dummy atoms in a topology. Another doubt is what would be the option need to be set in mdp file for " *couple-lambda1*" when we do free energy perturbation through B state topology: For example: At lambda=0, I have to use: couple-lambda0 vdw-q (all interactions are on at lambda=0 ) At lambda=1.0, I am not sure what should be the correct option: couple-lambda1 none; I think none will not work here since I am selectively turning off vdw and charges for few atoms by changing it to dummy atom in B state topology. On Sun, Feb 2, 2014 at 10:58 PM, Mark Abraham wrote: > On Sat, Feb 1, 2014 at 8:15 AM, bipin singh wrote: > > > Hello All, > > > > What is the meaning of the sentence " no idea what the mass should be" in > > atomtype.atp file of Gromos force field. > > > > "DUM 0.0 ; dummy atom, no idea what the mass should be. PT3-99" > > > > Is the mass of of dummy atom is always zero or something else. > > > > What we now call virtual sites in GROMACS were once called dummy atoms, so > it is possible that comment dates from that time. > > If during a free energy perturbation some atoms are converted into DUM > > atoms in the B state then how the bonded parameters (bond, angle > dihedral) > > will be affected. > > > I'm no expert here, but if you are making a particle disappear, then its > interactions will have to disappear in a consistent way. You can't have > forces on a particle that has no mass! Doubtless there is literature on the > correct kind of procedure. > > Mark > > > > > > -- > > > > > > > > *Thanks and Regards,Bipin Singh* > > -- > > 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. > -- *Thanks and Regards,Bipin Singh* -- 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] Regarding DUM atom in Gromos force field
Hello All, What is the meaning of the sentence " no idea what the mass should be" in atomtype.atp file of Gromos force field. "DUM 0.0 ; dummy atom, no idea what the mass should be. PT3-99" Is the mass of of dummy atom is always zero or something else. If during a free energy perturbation some atoms are converted into DUM atoms in the B state then how the bonded parameters (bond, angle dihedral) will be affected. -- *----Thanks and Regards,Bipin Singh* -- 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] g_helixorient help
Inter helical angle using *g_bundle * # 1. Do in make_ndx: # make_ndxGenerate indexes describing extremities of # the two helices. Select the CA of residues belonging #the extremities of each helix. make_ndx -f NAME.gro -o NAME_CROSSANGLE.ndx # Define other groups you need # Define 4 groups corresponding to the ends of the two helices # ... # q # 2. Do in a text editor: # Merge the 4 index groups, corresponding to helices ends, in order to get # two index groups, each containing either the beginning of the two # helices or the ends of the two helices. See g_bundle's online help. # The number of residues selected for each helix has to be the same. # 3. Do in g_bundle: # g_bundleGet coordinate of vectors describing the helices echo 0 1 | g_bundle -f NAME.xtc -s NAME.tpr -n NAME_CROSSANGLE.ndx \ -dt XX -b -e -na 2 -oa NAME_CROSSANGLE.pdb\ >& g_bundle.CROSSANGLE.out # -na 2; there are two axes this time # -oa NAME_CROSSANGLE.pdb ; to get the coordinates of the axes and check the angles given by the software # rm, Remove some unuseful files genererated by g_bundle: rm bun_len.xvg bun_dist.xvg bun_z.xvg bun_tilt.vxg bun_tiltl.xvg bun_tiltr.xvg # The first time, it might be helpful to open NAME_CROSSANGLE.pdb in rasmol or # vmd to visualize the data you are handling and check wether you define your # index correctly... and also two understand the structures of the data you # are handling. # The next part is dirty and could be automated with a smart script: # 4. Do in g_ traj # g_traj transform the .pdb trajectory in a file format easier to handle, # i.e a .xvg file. echo 0 | g_traj -f NAME_CROSSANGLE.pdb -s NAME_CROSSANGLE.pdb \ -ox NAME_CROSSANGLE.xvg >& g_traj.CROSSANGLE.out #In the header of the .xvg file, you have this: # @ legend string 0 "atom 1 X" # @ legend string 1 "atom 1 Y" # @ legend string 2 "atom 1 Z" # @ legend string 3 "atom 2 X" # @ legend string 4 "atom 2 Y" # @ legend string 5 "atom 2 Z" # @ legend string 6 "atom 3 X" # @ legend string 7 "atom 3 Y" # @ legend string 8 "atom 3 Z" # @ legend string 9 "atom 4 X" # @ legend string 10 "atom 4 Y" # @ legend string 11 "atom 4 Z" # @ legend string 12 "atom 5 X" # @ legend string 13 "atom 5 Y" # @ legend string 14 "atom 5 Z" # @ legend string 15 "atom 6 X" # @ legend string 16 "atom 6 Y" # @ legend string 17 "atom 6 Z" # 01.35431.23062.11210.85610.8589... # 201.40021.06922.04280.89430.7557... # 401.3591.07932.13410.86860.7528... # ...... # 5. Do in Microsoft Excel or equivalent # Import the .xvg file. You'll get a 19-column file. The first column # correspond to the time. The next 9 columns are (x,y,z) coordinates of 3 # points belonging to the vector describing the first helix and the next 9 # are coordinate of 3 points belonging to the second helix. # When this point is reached, you can define the vectors describing the # helices (by substracting coordinate of atom 3 and 1 and atom 6 and 4), # normalize them (by dividing the vector by their norm) and calulate their # dot-product in excel. # The dot product of two normalized vectors is the cosine of their # cross-angle. Disclaimer: Copied from an old gromacs discussion. On Thu, Jan 30, 2014 at 2:06 PM, rajat desikan wrote: > Hi All, > Any suggestions? > > Thanks. > > > On Mon, Jan 27, 2014 at 5:01 PM, rajat desikan >wrote: > > > Hi All, > > I am trying to calculate the angle between the axes of two alpha helices > > (say A and B) in my simulation. I have separate index files for the > > residues pertaining to each helix. > > > > I calculated the tilt.xvg for both A and B. The output is slightly > > confusing. tilt_A.xvg when viewed with xmgrace -nxy shows 27 data sets. > > What do these correspond to? (Helix A has 34 residues). Similarly for > > bending_A.xvg > > > > How do I go about this? Is this the right way to calculate the relative > > helix axis angle? > > > > Thanks, > > > > -- > > Rajat Desikan (Ph.D Scholar) > > Prof. K. Ganapathy Ayappa's Lab (no 13), > > Dept. of Chemical Engineering, > > Indian Institute of Science, Bangalore > > > > > > -- > Rajat Desikan (Ph.D Scholar) > Prof. K. Ganapathy Ayappa's Lab (no 13), > Dept. of Chemical Engineering, > Indian Institute of Science, Bangalore > -- > 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://w
Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
I think the corresponding dihedral (involving the HE2 atom) also need to be changed in the B state during the transformation. On Thu, Jan 30, 2014 at 9:48 PM, Justin Lemkul wrote: > > > On 1/30/14, 11:12 AM, bipin singh wrote: > >> The protonated and deprotonated states will differ only in terms of >> presence or absence of hydrogens, thus in B state only that hydrogen atom >> which is intended to be transformed from protonated to deprotonated state >> will be altered in the terms of electrostatic and vdw parameters. >> >> > Incorrect. The atom types and charges for the whole carboxylate moiety > are affected by the removal of the proton. Only H becomes a dummy atom, > but the C and both O atoms of the resulting COO- group will be different > depending on protonation state. See GLU/GLUH in aminoacids.rtp. > > -Justin > > > >> On Thu, Jan 30, 2014 at 8:55 PM, Ozbil, Mehmet >> wrote: >> >> I see Bipin, >>> >>> Thanks. One quick question though, am I going to change the charges to >>> zero or all atoms to DUM atoms for all the atoms in B state or just for >>> the >>> hydrogen that will be transferred between the states (the atom where the >>> B >>> state was missing before): >>> >>> 16 opls_270 77GLUHE2 5 0.45 1.008 >>> >>> Thanks again. >>> >>> Mehmet >>> >>> >>> >>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of bipin >>> singh >>> Sent: Wednesday, January 29, 2014 10:46 PM >>> To: Discussion list for GROMACS users >>> Subject: Re: [gmx-users] free energy calculations for reference state for >>> constant pH MD simulations... >>> >>> You have to define the B state parameters for your deprotonated state >>> explicitly. >>> >>> The following line in your topology does not have the parameters for the >>> B >>> state. >>> >>> 16 opls_270 77GLUHE2 5 0.45 1.008 >>> >>> You have to set the charges zero in the B state (if you want to consider >>> the change in electrostatic term only during deprotonation) or else >>> change >>> it to DUM atom (if you want to change both the vdw and electrostatics >>> terms >>> during deprotonation). >>> >>> >>> On Wed, Jan 29, 2014 at 8:15 PM, Ozbil, Mehmet >>> wrote: >>> >>> >>>> Thanks Bipin for the reply. >>>> >>>> I went through the Gromacs manual, and thought that I managed to >>>> incorporate two states (protonated and deprotonated) in my topology >>>> file. >>>> Can anyone who has done it before tell me if I defined both A and B >>>> >>> states >>> >>>> correctly in my .top file. >>>> >>>> ; >>>> ; File 'GLUA_prot_OPLS_p.top' was generated >>>> ; By user: onbekend (0) >>>> ; On host: onbekend >>>> ; At date: Tue Jan 28 13:49:17 2014 >>>> ; >>>> ; This is a standalone topology file >>>> ; >>>> ; It was generated using program: >>>> ; pdb2gmx - VERSION 4.5.4 >>>> ; >>>> ; Command line was: >>>> ; /home/apps/fas/Apps/Gromacs/gromacs-4.5.4-intel/bin//pdb2gmx -f >>>> GLUA_prot_OPLS.pdb -p GLUA_prot_OPLS_p.top -o GLUA_prot_OPLS_p.gro >>>> -inter >>>> ; >>>> ; Force field was read from the standard Gromacs share directory. >>>> ; >>>> >>>> ; Include forcefield parameters >>>> #include "oplsaa.ff/forcefield.itp" >>>> >>>> [ moleculetype ] >>>> ; Namenrexcl >>>> Protein_chain_A 3 >>>> >>>> [ atoms ] >>>> ; nr type resnr residue atom cgnr charge mass >>>> >>> typeB >>> >>>> chargeB massB >>>> ; residue 77 GLU rtp GLUH q 0.0 >>>> 1 opls_287 77GLU N 1 -0.314.0067 >>>> opls_287 -0.3 14.0067 >>>> 2 opls_290 77GLU H1 1 0.33 1.008 >>>> opls_2900.33 1.008 >>>> 3 opls_290 77GLU H2 1 0.3
Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
Thanks Dr. Justin for mentioning this important point. On Thu, Jan 30, 2014 at 9:48 PM, Justin Lemkul wrote: > > > On 1/30/14, 11:12 AM, bipin singh wrote: > >> The protonated and deprotonated states will differ only in terms of >> presence or absence of hydrogens, thus in B state only that hydrogen atom >> which is intended to be transformed from protonated to deprotonated state >> will be altered in the terms of electrostatic and vdw parameters. >> >> > Incorrect. The atom types and charges for the whole carboxylate moiety > are affected by the removal of the proton. Only H becomes a dummy atom, > but the C and both O atoms of the resulting COO- group will be different > depending on protonation state. See GLU/GLUH in aminoacids.rtp. > > -Justin > > > >> On Thu, Jan 30, 2014 at 8:55 PM, Ozbil, Mehmet >> wrote: >> >> I see Bipin, >>> >>> Thanks. One quick question though, am I going to change the charges to >>> zero or all atoms to DUM atoms for all the atoms in B state or just for >>> the >>> hydrogen that will be transferred between the states (the atom where the >>> B >>> state was missing before): >>> >>> 16 opls_270 77GLUHE2 5 0.45 1.008 >>> >>> Thanks again. >>> >>> Mehmet >>> >>> >>> >>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of bipin >>> singh >>> Sent: Wednesday, January 29, 2014 10:46 PM >>> To: Discussion list for GROMACS users >>> Subject: Re: [gmx-users] free energy calculations for reference state for >>> constant pH MD simulations... >>> >>> You have to define the B state parameters for your deprotonated state >>> explicitly. >>> >>> The following line in your topology does not have the parameters for the >>> B >>> state. >>> >>> 16 opls_270 77GLUHE2 5 0.45 1.008 >>> >>> You have to set the charges zero in the B state (if you want to consider >>> the change in electrostatic term only during deprotonation) or else >>> change >>> it to DUM atom (if you want to change both the vdw and electrostatics >>> terms >>> during deprotonation). >>> >>> >>> On Wed, Jan 29, 2014 at 8:15 PM, Ozbil, Mehmet >>> wrote: >>> >>> >>>> Thanks Bipin for the reply. >>>> >>>> I went through the Gromacs manual, and thought that I managed to >>>> incorporate two states (protonated and deprotonated) in my topology >>>> file. >>>> Can anyone who has done it before tell me if I defined both A and B >>>> >>> states >>> >>>> correctly in my .top file. >>>> >>>> ; >>>> ; File 'GLUA_prot_OPLS_p.top' was generated >>>> ; By user: onbekend (0) >>>> ; On host: onbekend >>>> ; At date: Tue Jan 28 13:49:17 2014 >>>> ; >>>> ; This is a standalone topology file >>>> ; >>>> ; It was generated using program: >>>> ; pdb2gmx - VERSION 4.5.4 >>>> ; >>>> ; Command line was: >>>> ; /home/apps/fas/Apps/Gromacs/gromacs-4.5.4-intel/bin//pdb2gmx -f >>>> GLUA_prot_OPLS.pdb -p GLUA_prot_OPLS_p.top -o GLUA_prot_OPLS_p.gro >>>> -inter >>>> ; >>>> ; Force field was read from the standard Gromacs share directory. >>>> ; >>>> >>>> ; Include forcefield parameters >>>> #include "oplsaa.ff/forcefield.itp" >>>> >>>> [ moleculetype ] >>>> ; Namenrexcl >>>> Protein_chain_A 3 >>>> >>>> [ atoms ] >>>> ; nr type resnr residue atom cgnr charge mass >>>> >>> typeB >>> >>>> chargeB massB >>>> ; residue 77 GLU rtp GLUH q 0.0 >>>> 1 opls_287 77GLU N 1 -0.314.0067 >>>> opls_287 -0.3 14.0067 >>>> 2 opls_290 77GLU H1 1 0.33 1.008 >>>> opls_2900.33 1.008 >>>> 3 opls_290 77GLU H2 1 0.33 1.008 >>>> opls_2900.33 1.008 >>>&
Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
The protonated and deprotonated states will differ only in terms of presence or absence of hydrogens, thus in B state only that hydrogen atom which is intended to be transformed from protonated to deprotonated state will be altered in the terms of electrostatic and vdw parameters. On Thu, Jan 30, 2014 at 8:55 PM, Ozbil, Mehmet wrote: > I see Bipin, > > Thanks. One quick question though, am I going to change the charges to > zero or all atoms to DUM atoms for all the atoms in B state or just for the > hydrogen that will be transferred between the states (the atom where the B > state was missing before): > > 16 opls_270 77GLUHE2 5 0.45 1.008 > > Thanks again. > > Mehmet > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of bipin > singh > Sent: Wednesday, January 29, 2014 10:46 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] free energy calculations for reference state for > constant pH MD simulations... > > You have to define the B state parameters for your deprotonated state > explicitly. > > The following line in your topology does not have the parameters for the B > state. > > 16 opls_270 77GLUHE2 5 0.45 1.008 > > You have to set the charges zero in the B state (if you want to consider > the change in electrostatic term only during deprotonation) or else change > it to DUM atom (if you want to change both the vdw and electrostatics terms > during deprotonation). > > > On Wed, Jan 29, 2014 at 8:15 PM, Ozbil, Mehmet wrote: > > > > > Thanks Bipin for the reply. > > > > I went through the Gromacs manual, and thought that I managed to > > incorporate two states (protonated and deprotonated) in my topology file. > > Can anyone who has done it before tell me if I defined both A and B > states > > correctly in my .top file. > > > > ; > > ; File 'GLUA_prot_OPLS_p.top' was generated > > ; By user: onbekend (0) > > ; On host: onbekend > > ; At date: Tue Jan 28 13:49:17 2014 > > ; > > ; This is a standalone topology file > > ; > > ; It was generated using program: > > ; pdb2gmx - VERSION 4.5.4 > > ; > > ; Command line was: > > ; /home/apps/fas/Apps/Gromacs/gromacs-4.5.4-intel/bin//pdb2gmx -f > > GLUA_prot_OPLS.pdb -p GLUA_prot_OPLS_p.top -o GLUA_prot_OPLS_p.gro -inter > > ; > > ; Force field was read from the standard Gromacs share directory. > > ; > > > > ; Include forcefield parameters > > #include "oplsaa.ff/forcefield.itp" > > > > [ moleculetype ] > > ; Namenrexcl > > Protein_chain_A 3 > > > > [ atoms ] > > ; nr type resnr residue atom cgnr charge mass > typeB > >chargeB massB > > ; residue 77 GLU rtp GLUH q 0.0 > > 1 opls_287 77GLU N 1 -0.314.0067 > > opls_287 -0.3 14.0067 > > 2 opls_290 77GLU H1 1 0.33 1.008 > > opls_2900.33 1.008 > > 3 opls_290 77GLU H2 1 0.33 1.008 > > opls_2900.33 1.008 > > 4 opls_290 77GLU H3 1 0.33 1.008 > > opls_2900.33 1.008 > > 5 opls_299 77GLU CA 1 0.15 12.011 > > opls_2990.15 12.011 > > 6 opls_140 77GLU HA 1 0.06 1.008 > > opls_1400.06 1.008 > > 7 opls_136 77GLU CB 2 -0.12 12.011 > > opls_136 -0.12 12.011 > > 8 opls_140 77GLUHB1 2 0.06 1.008 > > opls_1400.06 1.008 > > 9 opls_140 77GLUHB2 2 0.06 1.008 > > opls_1400.06 1.008 > > 10 opls_136 77GLU CG 3 -0.12 12.011 > > opls_136 -0.12 12.011 > > 11 opls_140 77GLUHG1 3 0.06 1.008 > > opls_1400.06 1.008 > > 12 opls_140 77GLUHG2 3 0.06 1.008 > > opls_1400.06 1.008 > > 13 opls_267 77GLU CD 4 0.52 12.011 > > opls_2670.52 12.011 > > 14 opls_269 77GLUOE1 4 -0.4415.9994 > > opls_269 -0.44 15.9994 > > 15 opls_268 77GLUOE2 5 -0.5315.9994 > > opls_268 -0.53 15.9994
Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
> 719 1 > 811 1 > 812 1 > 813 1 > 817 1 > 911 1 > 912 1 > 913 1 > 917 1 >1016 1 >1017 1 >1114 1 >1115 1 >1214 1 >1215 1 >1416 1 > > [ angles ] > ; aiajak functc0c1c2 >c3 > 2 1 3 1 > 2 1 4 1 > 2 1 5 1 > 3 1 4 1 > 3 1 5 1 > 4 1 5 1 > 1 5 6 1 > 1 5 7 1 > 1 517 1 > 6 5 7 1 > 6 517 1 > 7 517 1 > 5 7 8 1 > 5 7 9 1 > 5 710 1 > 8 7 9 1 > 8 710 1 > 9 710 1 > 71011 1 > 71012 1 > 71013 1 >111012 1 >111013 1 >121013 1 >101314 1 >101315 1 >141315 1 > 131516 1 > 51718 1 > 51719 1 >181719 1 > > [ dihedrals ] > ; aiajakal functc0c1c2 > c3c4c5 > 2 1 5 6 3 > 2 1 5 7 3 > 2 1 517 3 > 3 1 5 6 3 > 3 1 5 7 3 > 3 1 517 3 > 4 1 5 6 3 > 4 1 5 7 3 > 4 1 517 3 > 1 5 710 3dih_GLU_chi1_N_C_C_C >17 5 710 3dih_GLU_chi1_C_C_C_CO > 1 5 7 8 3 > 1 5 7 9 3 > 6 5 7 8 3 > 6 5 7 9 3 > 6 5 710 3 >17 5 7 8 3 >17 5 7 9 3 > 1 51718 3 > 1 51719 3 > 6 51718 3 > 6 51719 3 > 7 51718 3 > 7 51719 3 > 5 71011 3 > 5 71012 3 > 5 71013 3 > 8 71011 3 > 8 71012 3 > 8 71013 3 > 9 71011 3 > 9 71012 3 > 9 71013 3 > 7101314 3 > 7101315 3 >11101314 3 >11101315 3 >12101314 3 >12101315 3 >10131516 3dih_sidechain_COOH_C_C_O_H > 14131516 3dih_sidechain_COOH_O_C_O_H > > [ dihedrals ] > ; aiajakal functc0c1c2 > c3 > 5181719 1improper_O_C_X_Y >10141315 1improper_O_C_X_Y > > ; Include Position restraint file > #ifdef POSRES > #include "posre.itp" > #endif > > ; Include water topology > #include "oplsaa.ff/tip3p.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcxfcyfcz >11 1000 1000 1000 > #endif > > ; Include topology for ions > #include "oplsaa.ff/ions.itp" > > [ system ] > ; Name > Protein in water > > [ molecules ] > ; Compound#mols > Protein_chain_A 1 > SOL 4135 > > > Thanks, > Mehmet > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of bipin > singh > Sent: Tuesday, January 28, 2014 2:46 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] free energy calculations for reference state for > constant pH MD simulations... > > See the section "5.7.4 Topologies for free energy calculations" in Gromacs > 4.6.5 manual. > > > > On Tue, Jan 28, 2014 at 3:09 AM, Ozbil, Mehmet wrote: > > > Hello, > > > > I am trying to run constant pH MD with GROMACS, and started with the TI > > free energy calculations. I am following Justin Lemkul`s free energy > > calculation tutorial, and assuming that the free energy calculations will > > be similar to calculate the protonation energy of titratable amino acids > > such as GLU or HIS. > > > > My question is
Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
See the section "5.7.4 Topologies for free energy calculations" in Gromacs 4.6.5 manual. On Tue, Jan 28, 2014 at 3:09 AM, Ozbil, Mehmet wrote: > Hello, > > I am trying to run constant pH MD with GROMACS, and started with the TI > free energy calculations. I am following Justin Lemkul`s free energy > calculation tutorial, and assuming that the free energy calculations will > be similar to calculate the protonation energy of titratable amino acids > such as GLU or HIS. > > My question is that, while scanning the lambda values for the free energy > calculations do I need to define both protonated and deprotonated states of > GLU in the same .top and .pdb file, or I just use one .top and one .pdb > file and by changing the lambda values from 0.0 to 1.0 it does the > deprotonation itself. If I need to incorporate the two states in one .top > and .pdb file can anyone help with how to do that? > > Thanks, > Mehmet Ozbil > -- > 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. > -- *Thanks and Regards,Bipin Singh* -- 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] Free energy perturbation parameters sc-alpha sc-power sc-sigma
Ok, now I understand the transformation scheme. I think for doing the mentioned transformation you have to do the following things: 1) In the first set of transformation, transform the HG1 (1,2 and 3) and HG2 (1,2 and 3) to dummy atoms (you have written "I have to turn on the HG" can you explain why?) by first relaxing the coulombic terms (first transformation) followed by another transformation to relax the vdw terms (in a separate transformation). 2) Then transform your CG1 and CG2 atoms to HB atoms in another set of transformations. During these transformation you have to choose the spacing between the lambda values wisely based on some previous studies reported in literature for similar type of transformation. Also the soft core parameters during the (1) and (2) transformation should be set accrodingly. On Thu, Jan 23, 2014 at 2:44 PM, Francesca Vitalini < francesca.vitalin...@gmail.com> wrote: > Hi, > > thank you for the response, > > > Il giorno 23/gen/2014, alle ore 06:35, bipin singh > ha scritto: > > >> I am trying to perform a series of simulations where I gradually > transform > >> a valine capped amino acid (Ac-VAL-NHMe) into an alanine capped amino > acid > >> (Ac-ALA-NHMe), ie I have to turn on the HG and transform CG into HB. I > have > >> defined 6 lambda values at which I would like to equilibrate my system > >> (lambda=0,0.2,0.40.6,0.8,1) > > > > Would it not be better if you turn off the vdw and coul. terms of CG (1 > > atom) and HG (two atoms) and transform one of the HG to HB while doing > the > > transformation from valine to alanine, rather than mutating the CG to HB. > > > > If I transform a HG into a HB then won't I have problems with the bonds > definitions? How should I change my topology in order to define that in the > end state the mutated HG has to be bound to CB instead? > > Thank you very much. > > Francesca > > > > > On Wed, Jan 22, 2014 at 9:40 PM, Francesca Vitalini < > > francesca.vitalin...@gmail.com> wrote: > > > >> Dear Gromacs users, > >> > >> I am trying to perform a series of simulations where I gradually > transform > >> a valine capped amino acid (Ac-VAL-NHMe) into an alanine capped amino > acid > >> (Ac-ALA-NHMe), ie I have to turn on the HG and transform CG into HB. I > have > >> defined 6 lambda values at which I would like to equilibrate my system > >> (lambda=0,0.2,0.40.6,0.8,1) > >> > >> I am using GROMACS.4.5.5. and OPLS-AA force field. > >> > >> I have been following the tutorial by Justin Lemkul > >> > >> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html > >> > >> I have problems with the nvt equilibration with lambda=0.8 and lambda=1 > as > >> my systems systematically crashes. I believe that the reason is in the > >> tuning of the parameters sc-alpha sc-power sc-sigma in the mdp file. > >> I understand from the manual that sc_sigma should not be the default > option > >> as I have 6 hydrogens disappearing, and consequently the sc-alpha > sc-power > >> parameters will be effected as the interactions of the hydrogens in the > >> soft core state will get stronger. > >> However I have no experience in how to select these parameters and would > >> like to ask, if anyone has more experience, which could be plausible > >> values. > >> > >> Thank you very much, > >> > >> Francesca > >> > >> > >> For completeness I attach here a copy of my topology and mdp files. > >> > >> > >> TOPOLOGY > >> > >> > >> ; Include forcefield parameters > >> #include "oplsaa.ff/forcefield.itp" > >> > >> [ moleculetype ] > >> ; Namenrexcl > >> Protein_chain_A 3 > >> > >> [ atoms ] > >> ; nr type resnr residue atom cgnr charge mass > >> typeBchargeB massB > >> ; residue 1 ACE rtp ACE q 0.0 > >> 1 opls_135 1ACECH3 1 -0.18 12.011 > >> opls_135 -0.18 12.011 > >> 2 opls_140 1ACE HH31 1 0.06 1.008 > >> opls_140 0.06 1.008 > >> 3 opls_140 1ACE HH32 1 0.06 1.008 > >> opls_140 0.06 1.008 > >> 4 opls_140 1ACE HH33 1 0.06 1.008 > >> opls_140 0.06 1.008 > >> 5 opls_235 1ACE C 2
Re: [gmx-users] Free energy perturbation parameters sc-alpha sc-power sc-sigma
= yes > gen_temp = 300 > gen_seed = -1 > ; options for bonds > constraints = h-bonds ; we only have C-H bonds here > ; Type of constraint algorithm > constraint-algorithm = lincs > ; Do not constrain the starting configuration > continuation = no > ; Highest order in the expansion of the constraint coupling matrix > lincs-order = 12 > > > NVT_VDW.mdp > here I intend to switch off the Van der Waals interactions. The only > difference with the previous file is in the Free energy parameters, so I > will report only those. > > ; Free energy control stuff > free_energy = yes > init_lambda = 0.8 > delta_lambda = 0 > sc-alpha = 0.5 > sc-power = 1.0 > sc-sigma = 0.3 > couple-moltype = Protein_chain_A ; name of moleculetype to > decouple > couple-lambda0 = vdw ; only van der Waals interactions > couple-lambda1 = none ; turn off everything, in this case > only vdW > -- > 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. > -- *Thanks and Regards,Bipin Singh* -- 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] non-native contatcs
Once you identify the number and identity of the non-native contacts (after comparing the two matrices), then you can extract the probability of their formation from your trajectory. On Mon, Jan 20, 2014 at 8:23 PM, suhani nagpal wrote: > okay. > > Basically i want to make a plot these non-native contacts information which > are formed. > > some insights please > > Thanks > > > On Mon, Jan 20, 2014 at 7:33 PM, bipin singh wrote: > > > >so, now I need to compare the two contact matrices? ( one of native and > > >the other after 200ns) > > >as in superimpose or just by observing? > > In principle yes, you can get it both way i.e. by comparing the two > > matrices visually or mathematically, it depends what information you are > > looking for. > > > > > > On Mon, Jan 20, 2014 at 5:36 PM, suhani nagpal > >wrote: > > > > > Hey Bipin > > > > > > Thanks. yes, I have calculated the native contacts as well as the > > fraction > > > of native contacts using the vmd extension earlier. > > > > > > so, now I need to compare the two contact matrices? ( one of native > and > > > the other after 200ns) > > > > > > as in superimpose or just by observing? > > > > > > Thanks > > > > > > > > > On Wed, Jan 15, 2014 at 10:16 PM, rajat desikan < > rajatdesi...@gmail.com > > > >wrote: > > > > > > > Hi, > > > > I have never done this before. But is this a possibility? > > > > > > > > http://www.pymolwiki.org/index.php/Contact_map_visualizer > > > > > > > > > > > > On Wed, Jan 15, 2014 at 8:41 PM, bipin singh > > > wrote: > > > > > > > > > Hello Dr. Justin, > > > > > > > > > > Yes, there is no in-built module in Gromacs to get the information > > > about > > > > > native contacts during the simulation, but I think it can be done > > using > > > > the > > > > > following resources outside the Gromacs: > > > > > > > > > > > > > > > > > > > > > > > > > http://pythonhosted.org/MDAnalysis/documentation_pages/analysis/contacts.html > > > > > > > > > > http://www.multiscalelab.org/utilities/RMSDTTNC > > > > > > > > > > > > > > > On Wed, Jan 15, 2014 at 7:38 PM, Justin Lemkul > > > wrote: > > > > > > > > > > > > > > > > > > > > > > > On 1/15/14, 7:11 AM, bipin singh wrote: > > > > > > > > > > > >> First define and calculate the native contacts (contacts which > > were > > > > > >> present > > > > > >> in native reference structure and exist for significant amount > of > > > time > > > > > >> during simulation). Then you can identify the contacts which > exist > > > for > > > > > >> significant amount of time but were not present in native > > reference > > > > > >> structure (which may correspond to non-native contacts). > > > > > >> > > > > > >> > > > > > > Can you actually do this within Gromacs, or outside software? > I'd > > be > > > > > > curious to know. > > > > > > > > > > > > -Justin > > > > > > > > > > > > > > > > > > > > > > > >> > > > > > >> On Wed, Jan 15, 2014 at 1:05 PM, suhani nagpal < > > > > suhani.nag...@gmail.com > > > > > > > > > > > >> wrote: > > > > > >> > > > > > >> Greetings > > > > > >>> > > > > > >>> I'm studying protein unfolding by CTMD and REMD simulations to > > > > capture > > > > > >>> the > > > > > >>> intermediate states. > > > > > >>> > > > > > >>> I want to calculate the non-native contacts formed during the > > > > > >>> intermediate > > > > > >>> state. > > > > > >>> > > > > > >>> Suggestions please > > > > > >>> > > > > > >>> > > > > > >>> Thanks >
Re: [gmx-users] non-native contatcs
>so, now I need to compare the two contact matrices? ( one of native and >the other after 200ns) >as in superimpose or just by observing? In principle yes, you can get it both way i.e. by comparing the two matrices visually or mathematically, it depends what information you are looking for. On Mon, Jan 20, 2014 at 5:36 PM, suhani nagpal wrote: > Hey Bipin > > Thanks. yes, I have calculated the native contacts as well as the fraction > of native contacts using the vmd extension earlier. > > so, now I need to compare the two contact matrices? ( one of native and > the other after 200ns) > > as in superimpose or just by observing? > > Thanks > > > On Wed, Jan 15, 2014 at 10:16 PM, rajat desikan >wrote: > > > Hi, > > I have never done this before. But is this a possibility? > > > > http://www.pymolwiki.org/index.php/Contact_map_visualizer > > > > > > On Wed, Jan 15, 2014 at 8:41 PM, bipin singh > wrote: > > > > > Hello Dr. Justin, > > > > > > Yes, there is no in-built module in Gromacs to get the information > about > > > native contacts during the simulation, but I think it can be done using > > the > > > following resources outside the Gromacs: > > > > > > > > > > > > http://pythonhosted.org/MDAnalysis/documentation_pages/analysis/contacts.html > > > > > > http://www.multiscalelab.org/utilities/RMSDTTNC > > > > > > > > > On Wed, Jan 15, 2014 at 7:38 PM, Justin Lemkul > wrote: > > > > > > > > > > > > > > > On 1/15/14, 7:11 AM, bipin singh wrote: > > > > > > > >> First define and calculate the native contacts (contacts which were > > > >> present > > > >> in native reference structure and exist for significant amount of > time > > > >> during simulation). Then you can identify the contacts which exist > for > > > >> significant amount of time but were not present in native reference > > > >> structure (which may correspond to non-native contacts). > > > >> > > > >> > > > > Can you actually do this within Gromacs, or outside software? I'd be > > > > curious to know. > > > > > > > > -Justin > > > > > > > > > > > > > > > >> > > > >> On Wed, Jan 15, 2014 at 1:05 PM, suhani nagpal < > > suhani.nag...@gmail.com > > > > > > > >> wrote: > > > >> > > > >> Greetings > > > >>> > > > >>> I'm studying protein unfolding by CTMD and REMD simulations to > > capture > > > >>> the > > > >>> intermediate states. > > > >>> > > > >>> I want to calculate the non-native contacts formed during the > > > >>> intermediate > > > >>> state. > > > >>> > > > >>> Suggestions please > > > >>> > > > >>> > > > >>> Thanks > > > >>> Suhani > > > >>> Proteomics and Structural biology Lab > > > >>> CSIR-IGIB > > > >>> -- > > > >>> 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-usersor > > > >>> send a mail to gmx-users-requ...@gromacs.org. > > > >>> > > > >>> > > > >> > > > >> > > > >> > > > > -- > > > > == > > > > > > > > Justin A. Lemkul, Ph.D. > > > > Postdoctoral Fellow > > > > > > > > Department of Pharmaceutical Sciences > > > > School of Pharmacy > > > > Health Sciences Facility II, Room 601 > > > > University of Maryland, Baltimore > > > > 20 Penn St. > > > > Baltimore, MD 21201 > > > > > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > > > > > >
Re: [gmx-users] non-native contatcs
Hello Dr. Justin, Yes, there is no in-built module in Gromacs to get the information about native contacts during the simulation, but I think it can be done using the following resources outside the Gromacs: http://pythonhosted.org/MDAnalysis/documentation_pages/analysis/contacts.html http://www.multiscalelab.org/utilities/RMSDTTNC On Wed, Jan 15, 2014 at 7:38 PM, Justin Lemkul wrote: > > > On 1/15/14, 7:11 AM, bipin singh wrote: > >> First define and calculate the native contacts (contacts which were >> present >> in native reference structure and exist for significant amount of time >> during simulation). Then you can identify the contacts which exist for >> significant amount of time but were not present in native reference >> structure (which may correspond to non-native contacts). >> >> > Can you actually do this within Gromacs, or outside software? I'd be > curious to know. > > -Justin > > > >> >> On Wed, Jan 15, 2014 at 1:05 PM, suhani nagpal >> wrote: >> >> Greetings >>> >>> I'm studying protein unfolding by CTMD and REMD simulations to capture >>> the >>> intermediate states. >>> >>> I want to calculate the non-native contacts formed during the >>> intermediate >>> state. >>> >>> Suggestions please >>> >>> >>> Thanks >>> Suhani >>> Proteomics and Structural biology Lab >>> CSIR-IGIB >>> -- >>> 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. >>> >>> >> >> >> > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ====== > > -- > 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. > -- *Thanks and Regards,Bipin Singh* -- 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] non-native contatcs
First define and calculate the native contacts (contacts which were present in native reference structure and exist for significant amount of time during simulation). Then you can identify the contacts which exist for significant amount of time but were not present in native reference structure (which may correspond to non-native contacts). On Wed, Jan 15, 2014 at 1:05 PM, suhani nagpal wrote: > Greetings > > I'm studying protein unfolding by CTMD and REMD simulations to capture the > intermediate states. > > I want to calculate the non-native contacts formed during the intermediate > state. > > Suggestions please > > > Thanks > Suhani > Proteomics and Structural biology Lab > CSIR-IGIB > -- > 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. > -- *Thanks and Regards,Bipin Singh* -- 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] question regarding free energy calculations
Hello Dr. Justin, So, the option "couple-intramol = yes" can be used to selectively turn off vdw and coulombic interactions of only few atoms from the rest of the molecule using a B state topology in Gromacs, as mentioned by Asaf. On Thu, Dec 26, 2013 at 6:37 PM, Justin Lemkul wrote: > > > On 12/25/13, 4:55 AM, Asaf Farhi wrote: > >> Dear all >> >> Hi. We have a question regarding the implementation of free energy >> calculations in Gromacs that we have been trying for long time to decipher. >> >> The question is the following: >> >> When transforming molecule A to B if the non bonded interactions are >> changed through the topology file e.g: >> [ atoms ] >> ; nr type resnr resid atom cgnr chargemass typeB chargeB >> massB >> 1HC1 PCH3H110.123 1.0080 HC0.0 >> 1.0080 >> >> , will the the interactions of this atom with all the other atoms be >> affected by this change of charge? >> >> > That depends on how you are setting coupl-intramol (and on a related note, > check out http://redmine.gromacs.org/issues/1340). The nonbonded > interactions between the coupled molecule and its surroundings are > affected. Whether or not intramolecular interactions are affected depends > on coupl-intramol. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > > -- > 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. > -- *Thanks and Regards,Bipin Singh* -- 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] converting .xpm to .eps
Have you tried the first suggestion too ?? If even that does not worked then something wrong with your system. On Fri, Dec 20, 2013 at 5:06 PM, Nidhi Jatana wrote: > I tried increasing the grid spacing by setting -bin from default of 0.02 to > 0.04 and decreased it as well to 0.01. Butives the same of no help. It > still gives the same error. > > > On Fri, Dec 20, 2013 at 4:19 PM, bipin singh wrote: > > > You may try to produce the xpm matrix for small portion of your > trajectory > > (using -b and -e option) and then try xpm2ps on it to check whether it > > works for small size xpm matrix or not. > > > > OR you can increase the grid spacing with -bin option of g_densmap while > > generating the xpm matrix for the whole trajectory. > > > > > > On Fri, Dec 20, 2013 at 3:55 PM, Nidhi Jatana > >wrote: > > > > > How do you fix the matrix size? Should I do it while generation of .xpm > > > file or while converting it to .eps and using which option? > > > > > > Regards > > > Nidhi > > > > > > > > > On Fri, Dec 20, 2013 at 3:35 PM, Carsten Kutzner > > wrote: > > > > > > > On 12/20/2013 10:09 AM, bipin singh wrote: > > > > > > > >> Not sure, might be something going wrong due to large dimension of > > your > > > >> matrix. Which Gromacs version you are using. Others may provide some > > > >> clues. > > > >> > > > > I just tried with a 483 x 486 matrix which went smoothly. > > > > You could try to narrow down the problem. > > > > See whether it works with other input data for example. > > > > Check whether it works on another machine. > > > > > > > > Carsten > > > > > > > > > > > >> > > > >> On Fri, Dec 20, 2013 at 10:04 AM, Nidhi Jatana < > > > nidhijat...@bic-svc.ac.in > > > >> >wrote: > > > >> > > > >> Dear Sir/Madam > > > >>> Please find attached the file containing the error. > > > >>> > > > >>> Thanking you > > > >>> > > > >>> Regards > > > >>> -- > > > >>> Nidhi Jatana > > > >>> Senior Research Fellow > > > >>> Bioinformatics Center > > > >>> Sri Venkateswara College > > > >>> (University of Delhi) > > > >>> Dhaula Kuan > > > >>> New Delhi-110021. > > > >>> > > > >>> > > > >>> > > > >>> On Thu, Dec 19, 2013 at 7:44 PM, Carsten Kutzner > > > >>> wrote: > > > >>> > > > >>> On 12/19/2013 12:53 PM, Nidhi Jatana wrote: > > > >>>> > > > >>>> Dear Sir/Madam > > > >>>>> I generated the atomic density plot using g_densmap by giving the > > > >>>>> following > > > >>>>> command: > > > >>>>> g_densmap -f *.xtc -s *.pdb -n *.ndx -o *.xpm > > > >>>>> > > > >>>>> The calculation completed successfully but when I am trying to > > > convert > > > >>>>> .xpm > > > >>>>> file to .eps file using xpm2ps command, its giving error and > > aborts. > > > >>>>> > > > >>>>> What is the error message? > > > >>>> > > > >>>> If I use your set of commands with Gromacs 4.6.4, I can > successfully > > > >>>> > > > >>> create > > > >>> > > > >>>> an EPS file. > > > >>>> > > > >>>> Carsten > > > >>>> > > > >>>> > > > >>>> xpm2ps -f *.xpm -o *.eps -rainbow red -xpm *.xpm > > > >>>>> > > > >>>>> I have tried many options with setting -bx and -by but of no > help. > > I > > > >>>>> > > > >>>> also > > > >>> > > > >>>> tried taking the .m2p file but the problem persist. Please find > > > attached > > > >>>>> the .m2p file for reference. Please help me with this. > > > >>>>> > > > >>>>> Thanking you > > > >>>>> > > > >>>>> Regards > > > >
Re: [gmx-users] converting .xpm to .eps
You may try to produce the xpm matrix for small portion of your trajectory (using -b and -e option) and then try xpm2ps on it to check whether it works for small size xpm matrix or not. OR you can increase the grid spacing with -bin option of g_densmap while generating the xpm matrix for the whole trajectory. On Fri, Dec 20, 2013 at 3:55 PM, Nidhi Jatana wrote: > How do you fix the matrix size? Should I do it while generation of .xpm > file or while converting it to .eps and using which option? > > Regards > Nidhi > > > On Fri, Dec 20, 2013 at 3:35 PM, Carsten Kutzner wrote: > > > On 12/20/2013 10:09 AM, bipin singh wrote: > > > >> Not sure, might be something going wrong due to large dimension of your > >> matrix. Which Gromacs version you are using. Others may provide some > >> clues. > >> > > I just tried with a 483 x 486 matrix which went smoothly. > > You could try to narrow down the problem. > > See whether it works with other input data for example. > > Check whether it works on another machine. > > > > Carsten > > > > > >> > >> On Fri, Dec 20, 2013 at 10:04 AM, Nidhi Jatana < > nidhijat...@bic-svc.ac.in > >> >wrote: > >> > >> Dear Sir/Madam > >>> Please find attached the file containing the error. > >>> > >>> Thanking you > >>> > >>> Regards > >>> -- > >>> Nidhi Jatana > >>> Senior Research Fellow > >>> Bioinformatics Center > >>> Sri Venkateswara College > >>> (University of Delhi) > >>> Dhaula Kuan > >>> New Delhi-110021. > >>> > >>> > >>> > >>> On Thu, Dec 19, 2013 at 7:44 PM, Carsten Kutzner > >>> wrote: > >>> > >>> On 12/19/2013 12:53 PM, Nidhi Jatana wrote: > >>>> > >>>> Dear Sir/Madam > >>>>> I generated the atomic density plot using g_densmap by giving the > >>>>> following > >>>>> command: > >>>>> g_densmap -f *.xtc -s *.pdb -n *.ndx -o *.xpm > >>>>> > >>>>> The calculation completed successfully but when I am trying to > convert > >>>>> .xpm > >>>>> file to .eps file using xpm2ps command, its giving error and aborts. > >>>>> > >>>>> What is the error message? > >>>> > >>>> If I use your set of commands with Gromacs 4.6.4, I can successfully > >>>> > >>> create > >>> > >>>> an EPS file. > >>>> > >>>> Carsten > >>>> > >>>> > >>>> xpm2ps -f *.xpm -o *.eps -rainbow red -xpm *.xpm > >>>>> > >>>>> I have tried many options with setting -bx and -by but of no help. I > >>>>> > >>>> also > >>> > >>>> tried taking the .m2p file but the problem persist. Please find > attached > >>>>> the .m2p file for reference. Please help me with this. > >>>>> > >>>>> Thanking you > >>>>> > >>>>> Regards > >>>>>-- > >>>>> Nidhi Jatana > >>>>> Senior Research Fellow > >>>>> Bioinformatics Center > >>>>> Sri Venkateswara College > >>>>> (University of Delhi) > >>>>> Dhaula Kuan > >>>>> New Delhi-110021. > >>>>> > >>>>> > >>>>> > >>>>> -- > >>>> 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] converting .xpm to .eps
Not sure, might be something going wrong due to large dimension of your matrix. Which Gromacs version you are using. Others may provide some clues. On Fri, Dec 20, 2013 at 10:04 AM, Nidhi Jatana wrote: > Dear Sir/Madam > Please find attached the file containing the error. > > Thanking you > > Regards > -- > Nidhi Jatana > Senior Research Fellow > Bioinformatics Center > Sri Venkateswara College > (University of Delhi) > Dhaula Kuan > New Delhi-110021. > > > > On Thu, Dec 19, 2013 at 7:44 PM, Carsten Kutzner wrote: > > > On 12/19/2013 12:53 PM, Nidhi Jatana wrote: > > > >> Dear Sir/Madam > >> I generated the atomic density plot using g_densmap by giving the > >> following > >> command: > >> g_densmap -f *.xtc -s *.pdb -n *.ndx -o *.xpm > >> > >> The calculation completed successfully but when I am trying to convert > >> .xpm > >> file to .eps file using xpm2ps command, its giving error and aborts. > >> > > What is the error message? > > > > If I use your set of commands with Gromacs 4.6.4, I can successfully > create > > an EPS file. > > > > Carsten > > > > > >> xpm2ps -f *.xpm -o *.eps -rainbow red -xpm *.xpm > >> > >> I have tried many options with setting -bx and -by but of no help. I > also > >> tried taking the .m2p file but the problem persist. Please find attached > >> the .m2p file for reference. Please help me with this. > >> > >> Thanking you > >> > >> Regards > >> -- > >> Nidhi Jatana > >> Senior Research Fellow > >> Bioinformatics Center > >> Sri Venkateswara College > >> (University of Delhi) > >> Dhaula Kuan > >> New Delhi-110021. > >> > >> > >> > > -- > > 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. > > -- *Thanks and Regards,Bipin Singh* -- 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] MM/GBSA and MM/PBSA in gromacs module
You may want to look at the below article. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046902 On Tue, Dec 17, 2013 at 8:22 AM, wrote: > Ｉ have the same question， too！ > At 2013-12-16 22:48:06,"Arunima Shilpi" wrote: > >Dear Sir > > > >I had query as to whether the Gromacs provide the module to work on > MM/GBSA > >and MM/PBSA. If yes then kindly provide us the link to access it. > > > > > >Regards > > > >Arunima > >-- > >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. > -- *Thanks and Regards,Bipin Singh* -- 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] Fwd: converting .xpm to .eps
Without looking at exact errors no one can guess what is happening. Better to post the exact error you are getting while running xpm2ps. On Thu, Dec 19, 2013 at 5:35 PM, Nidhi Jatana wrote: > Dear Sir/Madam > I generated the atomic density plot using g_densmap by giving the following > command: > g_densmap -f *.xtc -s *.pdb -n *.ndx -o *.xpm > > The calculation completed successfully but when I am trying to convert .xpm > file to .eps file using xpm2ps command, its giving error and aborts. > > xpm2ps -f *.xpm -o *.eps -rainbow red -xpm *.xpm > > I have tried many options with setting -bx and -by but of no help. I also > tried taking the .m2p file but the problem persist. Please find attached > the .m2p file for reference. Please help me with this. > > Thanking you > > Regards > -- > Nidhi Jatana > Senior Research Fellow > Bioinformatics Center > Sri Venkateswara College > (University of Delhi) > Dhaula Kuan > New Delhi-110021. > > -- > 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. > > -- *Thanks and Regards,Bipin Singh* -- 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] Restarting crashed run
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts http://www.gromacs.org/Documentation/How-tos/Extending_Simulations On Thu, Dec 19, 2013 at 11:37 AM, Nidhi Katyal wrote: > Dear gromacs users > > I have a small query regarding restarting crashed run. If I have given > following command: > mdrun -s topol.tpr > i.e. without giving -cpi state.cpt , But my folder contains state.cpt, does > it automatically takes this input file from the folder? > Also, does the same thing holds true for extending simulations > (no crashed runs)? > Does this depends on version also (say from gromacs 4.0.7 till 4.6.3)? > > 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. > -- *Thanks and Regards,Bipin Singh* -- 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] Bin files of g_sham
t; Stephan Watkins > > >>>> *Gesendet:* Sonntag, 15. Dezember 2013 um 14:49 Uhr > > >>>> *Von:* "Ankita Naithani" > > >>>> *An:* "Discussion list for GROMACS users" > > >>>> *Betreff:* [gmx-users] Bin files of g_sham > > >> > > >>>> Hi, > > >>>> > > >>>> I had a query regarding the bin files generated by g_sham. > > >>>> Does the bin index contain timepoints? i.e. there are 1024 bins so > > each > > >>>> bin > > >>>> has a number of time points? And supposes bin 756 has numbers like > > 3876, > > >>>> 20020, 7896 so these would all correspond to time and we could then > > dump > > >>>> the representative frame corresponding to these time points? > > >>>> > > >>>> I am a little confused as to what is stored in the bins? Timepoints > or > > >>>> frame number and then alternatively how to get the representative > > >>>> frame/snapshot stored at that specific bin number. > > >>>> > > >>>> Kind regards, > > >>>> > > >>>> -- > > >>>> Ankita Naithani > > >>>> -- > > >>>> 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-usersor > > >>>> 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-usersor > > >>>> send a mail to gmx-users-requ...@gromacs.org. > > >>> > > >>> > > >>> -- > > >>> Ankita Naithani > > >> > > >> > > >> > > >> -- > > >> Ankita Naithani > > >> -- > > >> 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. > > > > > > > > > -- > > > Ankita Naithani > > > -- > > > 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. > > > > > > > -- > Ankita Naithani > -- > 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. > -- *Thanks and Regards,Bipin Singh* -- 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] Doubt in free energy calculation options
Dear all, I am trying to calculate relative free energies of hydration between two similar molecules. I want to do the following things: (1) Totally remove the VDW and Coulomb interactions of few atoms (remove their interaction with all atoms). (2) Transform the Coulomb term (partial charge) of few atoms to a certain value (such that this value will be the one relevant for the interactions with all the other atoms). If I understand correctly the (1) transformation can be implemented by turning the charges to zero in state B and further changing it to DUM atoms by another transformation. Could you please advise if the (2) option can be implemented through Gromacs free energy mdp options?. And what should be the "coupl-intramol" value to be used during these transformations (I do not want to decouple solute-solvent interaction during these transformations). Thanks in advance. -- *---- Regards,Bipin Singh* -- 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] Regarding relative free energy calculation
Dear all, I am trying to calculate relative free energies of hydration between two similar molecules. I want to do the following things: (1) Totally remove the VDW and Coulomb interactions of few atoms (remove their interaction with all atoms). (2) Transform the Coulomb term (partial charge) of few atoms to a certain value (such that this value will be the one relevant for the interactions with all the other atoms). If I understand correctly the (1) transformation can be implemented by turning the charges to zero in state B and further changing it to DUM atoms by another transformation. Could you please advise if the (2) option can be implemented through Gromacs free energy mdp options? Thanks in advance. -- *Regards,Bipin Singh* -- 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] Regarding Gromacs 5.0 Beta1 release
Thank You Prof. Shirts for your clarification. On Mon, Dec 9, 2013 at 9:40 PM, Michael Shirts wrote: > There's two issues here; an actual bug (#1315) with intramolecular 1-4 > interactions when combining function type 2 and 1, and the fact that > couple-intramol doesn't do exactly what you might expect it to do, > i.e.: right now, if one sets coupl-intramol = yes, LJ and Coul 1-4's > are left on (uncoupled) at all lambda. The actual bug is fixed in 5.0 > (actually, in 4.6.4). > > If you look in the discussion, then adding more flexibility is on the > short term plan. It is not in the beta current, but there is a good > chance this extra flexibility will be in the next test release and in > the final 5.0. If not, it will definitely be in 5.1. > > > On Mon, Dec 9, 2013 at 9:11 AM, bipin singh wrote: > > Hi, > > > > Please let me know whether the below issue (link) has been addressed in > this > > release: > > > > http://bugzilla.gromacs.org/issues/1340 > > > > If no then is there any plan to include this in future release. > > > > -- > > ---- > > Thanks and Regards, > > Bipin Singh > > > -- *Thanks and Regards,Bipin Singh* -- 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] Regarding Gromacs 5.0 Beta1 release
Hi, Please let me know whether the below issue (link) has been addressed in this release: http://bugzilla.gromacs.org/issues/1340 If no then is there any plan to include this in future release. -- *Thanks and Regards,Bipin Singh* -- 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] out of disk space error
If none of the earlier suggestions worked then, it could be a simple problem of power port from which you have connected your hard disk. Try reconnecting the hard disk and and retry running the mdrun. Posting the exact commands used while writing the output during mdrun, may help to trace the problem. On Thu, Dec 5, 2013 at 11:03 AM, vaani wrote: > > On 12/4/13 5:24 AM, amin@.res wrote: > > > > > > I think so. You are outputting the information too often i.e every 0.2 > > ps i.e. 5000 times per ns. See this thread > > > > http://comments.gmane.org/gmane.science.biology.gromacs.user/32721 > > > > It is unlikely that a few hundred ps of NVT would fill up someone's disk if > it > has several hundred GB available, but it can't hurt to reduce the output a > bit. > Frequent writing could be taxing the filesystem unnecessarily. > > It is also important to keep in mind that some desktop computers simply > cannot > handle a simulation that would be best run on a cluster with > high-performance I/O. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > hi justin, > i have already run simulations on this work station before also without any > such disk space problem. i am facing this problem now only after installing > ubuntu and gromacs freshly, > > best > > > > > - > thanks in advance :) > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013086.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.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. > -- *Thanks and Regards,Bipin Singh* -- 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] Regarding soft core parameter: Relative solvation free energy calculation
Thank you Prof. Shirts for your help and suggestions. On Sat, Nov 30, 2013 at 6:04 AM, Michael Shirts wrote: > The fluctuation is often of the order of magnitude of itself. > It's that matters. > > > > On Thu, Nov 28, 2013 at 1:26 PM, bipin singh wrote: > > Thanks for you reply Prof. Shirts. > > > > I have plotted the dh/dl values (link mentioned below), but I am not sure > > whether the fluctuation is in acceptable range at lambda=0.0. Please > have a > > look at the plot and let me know your thoughts. > > > > http://researchweb.iiit.ac.in/~bipin.singh/dhdl.png > > > > > > On Thu, Nov 28, 2013 at 8:44 PM, Michael Shirts > wrote: > > > >> It's very possible that this is entirely physical. dh/dl fluctuates a > >> lot. You may want to look at graphs of after a few 10's of ps > >> to see if it looks reasonable. > >> > >> On Thu, Nov 28, 2013 at 10:04 AM, bipin singh > >> wrote: > >> > I am mentioning below the average and standard deviation of dh/dl > values > >> at > >> > lambda=0.0 and lambda=1.0, for sc-alpha=0.5 > >> > > >> > Avg Std. > >> > lambda0.0-2.055812e+01 2.730571e+01 > >> > > >> > lambda1.07.086960e+017.670135e+00 > >> > > >> > > >> > On Thu, Nov 28, 2013 at 7:34 PM, bipin singh > >> wrote: > >> > > >> >> Thanks for the reply. > >> >> > >> >> By large fluctuations, I mean the standard deviation of dh/dl values > >> >> during the simulation at lambda 0.0 to 0.5 in comparison to lambda > >> close to > >> >> 1, when using sc-alpha=0.5 > >> >> > >> >> > >> >> On Thu, Nov 28, 2013 at 7:27 PM, Michael Shirts >> >wrote: > >> >> > >> >>> Define large fluctuations. They might be physical large > fluctuations! > >> >>> > >> >>> > >> >>> > >> >>> On Thu, Nov 28, 2013 at 1:19 AM, bipin singh > >> >>> wrote: > >> >>> > Hello All, > >> >>> > > >> >>> > I am trying to calculate relative solvation free energy for > p-Cresol > >> and > >> >>> > p-Chlorophenol using Gromacs 4.6.3. > >> >>> > > >> >>> > I am using equispaced lamda values viz. 0.1, 0.05, 0.1,, 1.0 > >> >>> > > >> >>> > During one transformation (lambda 0.0 to 1.0) I am switching off > the > >> vdW > >> >>> > terms (Changed to DUM atoms) for the -CH3 and -Cl group in > p-Cresol > >> amd > >> >>> > p-Chlorophenol respectively. > >> >>> > > >> >>> > Thus I am using a constant sc-alpha=0.5 at each lambda values > (0.0 to > >> >>> 1.0) > >> >>> > for both the molecules. > >> >>> > > >> >>> > But I am getting a large fluctuation in dh/dl values only at > initial > >> >>> lambda > >> >>> > values i.e. from 0.0 to 0.5, and only in the case of p-Cresol > (-CH3 > >> is > >> >>> > being changed to DUM). > >> >>> > > >> >>> > If I change the sc-alpha=0 for initial lamda ( i.e. from 0.0 to > >> 0.5), I > >> >>> get > >> >>> > consistent values of dh/dl (i.e. less deviation during > simulation). > >> >>> > > >> >>> > > >> >>> > Can anyone suggest the reason for this behaviour and how to select > >> >>> > appropriate values of sc-alpha based on transformation. And can we > >> use > >> >>> > different sets of sc-alpha values for two molecules to compute > their > >> >>> > relative solvation free energies. > >> >>> > > >> >>> > > >> >>> > > >> >>> > I have used the following mdp settings: > >> >>> > > >> >>> > sc-power = 1 > >> >>> > sc-alpha = 0.5 > >> >>> > sc-r-power = 6 > >> >>> > sc-coul = no > >> >>> > &g
Re: [gmx-users] Regarding soft core parameter: Relative solvation free energy calculation
Thanks for you reply Prof. Shirts. I have plotted the dh/dl values (link mentioned below), but I am not sure whether the fluctuation is in acceptable range at lambda=0.0. Please have a look at the plot and let me know your thoughts. http://researchweb.iiit.ac.in/~bipin.singh/dhdl.png On Thu, Nov 28, 2013 at 8:44 PM, Michael Shirts wrote: > It's very possible that this is entirely physical. dh/dl fluctuates a > lot. You may want to look at graphs of after a few 10's of ps > to see if it looks reasonable. > > On Thu, Nov 28, 2013 at 10:04 AM, bipin singh > wrote: > > I am mentioning below the average and standard deviation of dh/dl values > at > > lambda=0.0 and lambda=1.0, for sc-alpha=0.5 > > > > Avg Std. > > lambda0.0-2.055812e+01 2.730571e+01 > > > > lambda1.07.086960e+017.670135e+00 > > > > > > On Thu, Nov 28, 2013 at 7:34 PM, bipin singh > wrote: > > > >> Thanks for the reply. > >> > >> By large fluctuations, I mean the standard deviation of dh/dl values > >> during the simulation at lambda 0.0 to 0.5 in comparison to lambda > close to > >> 1, when using sc-alpha=0.5 > >> > >> > >> On Thu, Nov 28, 2013 at 7:27 PM, Michael Shirts >wrote: > >> > >>> Define large fluctuations. They might be physical large fluctuations! > >>> > >>> > >>> > >>> On Thu, Nov 28, 2013 at 1:19 AM, bipin singh > >>> wrote: > >>> > Hello All, > >>> > > >>> > I am trying to calculate relative solvation free energy for p-Cresol > and > >>> > p-Chlorophenol using Gromacs 4.6.3. > >>> > > >>> > I am using equispaced lamda values viz. 0.1, 0.05, 0.1,, 1.0 > >>> > > >>> > During one transformation (lambda 0.0 to 1.0) I am switching off the > vdW > >>> > terms (Changed to DUM atoms) for the -CH3 and -Cl group in p-Cresol > amd > >>> > p-Chlorophenol respectively. > >>> > > >>> > Thus I am using a constant sc-alpha=0.5 at each lambda values (0.0 to > >>> 1.0) > >>> > for both the molecules. > >>> > > >>> > But I am getting a large fluctuation in dh/dl values only at initial > >>> lambda > >>> > values i.e. from 0.0 to 0.5, and only in the case of p-Cresol (-CH3 > is > >>> > being changed to DUM). > >>> > > >>> > If I change the sc-alpha=0 for initial lamda ( i.e. from 0.0 to > 0.5), I > >>> get > >>> > consistent values of dh/dl (i.e. less deviation during simulation). > >>> > > >>> > > >>> > Can anyone suggest the reason for this behaviour and how to select > >>> > appropriate values of sc-alpha based on transformation. And can we > use > >>> > different sets of sc-alpha values for two molecules to compute their > >>> > relative solvation free energies. > >>> > > >>> > > >>> > > >>> > I have used the following mdp settings: > >>> > > >>> > sc-power = 1 > >>> > sc-alpha = 0.5 > >>> > sc-r-power = 6 > >>> > sc-coul = no > >>> > > >>> > > >>> > and > >>> > > >>> > > >>> > sc-power = 1 > >>> > sc-alpha = 0.0 > >>> > sc-r-power = 6 > >>> > sc-coul = no > >>> > > >>> > ### > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > *----Thanks and Regards,Bipin Singh* > >>> > -- > >>> > 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-usersor > >>> send a mail to gmx-users-requ...@gromacs.org. > >
Re: [gmx-users] Regarding soft core parameter: Relative solvation free energy calculation
I am mentioning below the average and standard deviation of dh/dl values at lambda=0.0 and lambda=1.0, for sc-alpha=0.5 Avg Std. lambda0.0-2.055812e+01 2.730571e+01 lambda1.07.086960e+017.670135e+00 On Thu, Nov 28, 2013 at 7:34 PM, bipin singh wrote: > Thanks for the reply. > > By large fluctuations, I mean the standard deviation of dh/dl values > during the simulation at lambda 0.0 to 0.5 in comparison to lambda close to > 1, when using sc-alpha=0.5 > > > On Thu, Nov 28, 2013 at 7:27 PM, Michael Shirts wrote: > >> Define large fluctuations. They might be physical large fluctuations! >> >> >> >> On Thu, Nov 28, 2013 at 1:19 AM, bipin singh >> wrote: >> > Hello All, >> > >> > I am trying to calculate relative solvation free energy for p-Cresol and >> > p-Chlorophenol using Gromacs 4.6.3. >> > >> > I am using equispaced lamda values viz. 0.1, 0.05, 0.1,, 1.0 >> > >> > During one transformation (lambda 0.0 to 1.0) I am switching off the vdW >> > terms (Changed to DUM atoms) for the -CH3 and -Cl group in p-Cresol amd >> > p-Chlorophenol respectively. >> > >> > Thus I am using a constant sc-alpha=0.5 at each lambda values (0.0 to >> 1.0) >> > for both the molecules. >> > >> > But I am getting a large fluctuation in dh/dl values only at initial >> lambda >> > values i.e. from 0.0 to 0.5, and only in the case of p-Cresol (-CH3 is >> > being changed to DUM). >> > >> > If I change the sc-alpha=0 for initial lamda ( i.e. from 0.0 to 0.5), I >> get >> > consistent values of dh/dl (i.e. less deviation during simulation). >> > >> > >> > Can anyone suggest the reason for this behaviour and how to select >> > appropriate values of sc-alpha based on transformation. And can we use >> > different sets of sc-alpha values for two molecules to compute their >> > relative solvation free energies. >> > >> > >> > >> > I have used the following mdp settings: >> > >> > sc-power = 1 >> > sc-alpha = 0.5 >> > sc-r-power = 6 >> > sc-coul = no >> > >> > >> > and >> > >> > >> > sc-power = 1 >> > sc-alpha = 0.0 >> > sc-r-power = 6 >> > sc-coul = no >> > >> > ### >> > >> > >> > >> > >> > >> > *Thanks and Regards,Bipin Singh* >> > -- >> > 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. >> > > > > -- > > > > *Thanks and Regards, Bipin Singh* > > -- *Thanks and Regards,Bipin Singh* -- 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] Regarding soft core parameter: Relative solvation free energy calculation
Thanks for the reply. By large fluctuations, I mean the standard deviation of dh/dl values during the simulation at lambda 0.0 to 0.5 in comparison to lambda close to 1, when using sc-alpha=0.5 On Thu, Nov 28, 2013 at 7:27 PM, Michael Shirts wrote: > Define large fluctuations. They might be physical large fluctuations! > > > > On Thu, Nov 28, 2013 at 1:19 AM, bipin singh wrote: > > Hello All, > > > > I am trying to calculate relative solvation free energy for p-Cresol and > > p-Chlorophenol using Gromacs 4.6.3. > > > > I am using equispaced lamda values viz. 0.1, 0.05, 0.1,, 1.0 > > > > During one transformation (lambda 0.0 to 1.0) I am switching off the vdW > > terms (Changed to DUM atoms) for the -CH3 and -Cl group in p-Cresol amd > > p-Chlorophenol respectively. > > > > Thus I am using a constant sc-alpha=0.5 at each lambda values (0.0 to > 1.0) > > for both the molecules. > > > > But I am getting a large fluctuation in dh/dl values only at initial > lambda > > values i.e. from 0.0 to 0.5, and only in the case of p-Cresol (-CH3 is > > being changed to DUM). > > > > If I change the sc-alpha=0 for initial lamda ( i.e. from 0.0 to 0.5), I > get > > consistent values of dh/dl (i.e. less deviation during simulation). > > > > > > Can anyone suggest the reason for this behaviour and how to select > > appropriate values of sc-alpha based on transformation. And can we use > > different sets of sc-alpha values for two molecules to compute their > > relative solvation free energies. > > > > > > > > I have used the following mdp settings: > > > > sc-power = 1 > > sc-alpha = 0.5 > > sc-r-power = 6 > > sc-coul = no > > > > > > and > > > > > > sc-power = 1 > > sc-alpha = 0.0 > > sc-r-power = 6 > > sc-coul = no > > > > ### > > > > > > > > > > > > *Thanks and Regards,Bipin Singh* > > -- > > 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. > -- *Thanks and Regards,Bipin Singh* -- 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] Regarding soft core parameter: Relative solvation free energy calculation
Hello All, I am trying to calculate relative solvation free energy for p-Cresol and p-Chlorophenol using Gromacs 4.6.3. I am using equispaced lamda values viz. 0.1, 0.05, 0.1,, 1.0 During one transformation (lambda 0.0 to 1.0) I am switching off the vdW terms (Changed to DUM atoms) for the -CH3 and -Cl group in p-Cresol amd p-Chlorophenol respectively. Thus I am using a constant sc-alpha=0.5 at each lambda values (0.0 to 1.0) for both the molecules. But I am getting a large fluctuation in dh/dl values only at initial lambda values i.e. from 0.0 to 0.5, and only in the case of p-Cresol (-CH3 is being changed to DUM). If I change the sc-alpha=0 for initial lamda ( i.e. from 0.0 to 0.5), I get consistent values of dh/dl (i.e. less deviation during simulation). Can anyone suggest the reason for this behaviour and how to select appropriate values of sc-alpha based on transformation. And can we use different sets of sc-alpha values for two molecules to compute their relative solvation free energies. I have used the following mdp settings: sc-power = 1 sc-alpha = 0.5 sc-r-power = 6 sc-coul = no and sc-power = 1 sc-alpha = 0.0 sc-r-power = 6 sc-coul = no ### *Thanks and Regards,Bipin Singh* -- 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] Warning while using g_bar
Thanks for your reply Szilard Pal. On Wed, Nov 27, 2013 at 7:34 PM, Szilárd Páll wrote: > On Wed, Nov 27, 2013 at 3:27 AM, bipin singh wrote: > > Hi all, > > > > While using g_bar I get the following warning for the below mentioned > > result. I know it is due to -ve entropy, but what "-0.00" denote > > That's just the nature of floating point numbers: > http://en.wikipedia.org/wiki/Signed_zero > > Cheers, > -- > Szilárd > > > > > WARNING: Some of these results violate the Second Law of Thermodynamics: > > This is can be the result of severe undersampling, or (more > likely) > > there is something wrong with the simulations. > > > > > > > > Samples in time interval: 0.000 - 1000.000 > > Removing samples outside of: 500.000 - 1000.000 > > > > Temperature: 300 K > > > > Detailed results in kT (see help for explanation): > > > > lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/- > > 0.000 0.0500.42 0.00 -0.00 0.00 -0.00 0.000.01 0.00 > > 0.050 0.1000.42 0.000.00 0.000.00 0.000.01 0.00 > > 0.100 0.2000.84 0.00 -0.00 0.00 -0.00 0.000.03 0.00 > > 0.200 0.3000.84 0.000.00 0.000.00 0.000.03 0.00 > > 0.300 0.4000.84 0.00 -0.00 0.00 -0.00 0.000.03 0.00 > > 0.400 0.5000.84 0.000.00 0.000.00 0.000.03 0.00 > > 0.500 0.6000.84 0.00 -0.00 0.00 -0.00 0.000.03 0.00 > > 0.600 0.7000.84 0.000.00 0.000.00 0.000.03 0.00 > > 0.700 0.8000.84 0.000.00 0.000.00 0.000.03 0.00 > > 0.800 0.9000.84 0.00 -0.00 0.00 -0.00 0.000.03 0.00 > > 0.900 1.0000.84 0.000.00 0.000.00 0.000.02 0.00 > > > > > > > > > > -- > > > > > > > > *Thanks and Regards,Bipin Singh* > > -- > > 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. > -- *Thanks and Regards,Bipin Singh* -- 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] Warning while using g_bar
Hi all, While using g_bar I get the following warning for the below mentioned result. I know it is due to -ve entropy, but what "-0.00" denote WARNING: Some of these results violate the Second Law of Thermodynamics: This is can be the result of severe undersampling, or (more likely) there is something wrong with the simulations. Samples in time interval: 0.000 - 1000.000 Removing samples outside of: 500.000 - 1000.000 Temperature: 300 K Detailed results in kT (see help for explanation): lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/- 0.000 0.0500.42 0.00 -0.00 0.00 -0.00 0.000.01 0.00 0.050 0.1000.42 0.000.00 0.000.00 0.000.01 0.00 0.100 0.2000.84 0.00 -0.00 0.00 -0.00 0.000.03 0.00 0.200 0.3000.84 0.000.00 0.000.00 0.000.03 0.00 0.300 0.4000.84 0.00 -0.00 0.00 -0.00 0.000.03 0.00 0.400 0.5000.84 0.000.00 0.000.00 0.000.03 0.00 0.500 0.6000.84 0.00 -0.00 0.00 -0.00 0.000.03 0.00 0.600 0.7000.84 0.000.00 0.000.00 0.000.03 0.00 0.700 0.8000.84 0.000.00 0.000.00 0.000.03 0.00 0.800 0.9000.84 0.00 -0.00 0.00 -0.00 0.000.03 0.00 0.900 1.0000.84 0.000.00 0.000.00 0.000.02 0.00 -- *Thanks and Regards,Bipin Singh* -- 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] Regarding soft-core potential
Thanks for the clarification Dr. Justin. Now it is clear to me. On Tue, Nov 26, 2013 at 8:29 PM, Justin Lemkul wrote: > On Tue, Nov 26, 2013 at 9:56 AM, bipin singh wrote: > > > Thanks for the reply Dr. Justin. > > > > Then is it not contrasting to the below statement, mentioned in online > > manual ? > > > > "the soft-core alpha parameter, a value of 0 results in linear > > interpolation of the LJ and Coulomb interactions" > > > > > No, that's not inconsistent. If sc_alpha > 0, then scale LJ with soft-core > and Coulomb linearly. If sc_alpha = 0, scale both LJ and Coulomb linearly. > > -Justin > > > > > > On Tue, Nov 26, 2013 at 6:35 PM, Justin Lemkul wrote: > > > > > On Tue, Nov 26, 2013 at 7:52 AM, bipin singh > > wrote: > > > > > > > Hello, > > > > > > > > Below is the text taken from the page number 97 of Gromacs 4.6.4 > > manual: > > > > > > > > "When soft core potentials are selected *(by setting sc-alpha ¿ 0)*, > > and > > > > the Coulomb and Lennard-Jones potentials are turned on or off > > > sequentially, > > > > then the Coulombic interaction is turned off linearly, rather than > > using > > > > soft core interactions, which should be less statistically noisy in > > most > > > > cases". > > > > > > > > *Doubt:* > > > > > > > > > > > > > > > > > > > > *sc-alpha ¿ 0 is actually sc-alpha=0 * > > > > Am I right ? > > > > > > > > > > > No. The bogus character should indicate "not equal to." > > > > > > -Justin > > > > > > -- > > > > > > == > > > > > > Justin A. Lemkul, Ph.D. > > > Postdoctoral Fellow > > > > > > Department of Pharmaceutical Sciences > > > School of Pharmacy > > > Health Sciences Facility II, Room 601 > > > University of Maryland, Baltimore > > > 20 Penn St. > > > Baltimore, MD 21201 > > > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > > > > > > > == > > > -- > > > 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. > > > > > > > > > > > -- > > > > > > *---Thanks and Regards,Bipin Singh* > > -- > > 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. > > > > > > -- > > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > == > -- > 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. > -- *---Thanks and Regards,Bipin Singh* -- 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] Regarding soft-core potential
Thanks for the reply Dr. Justin. Then is it not contrasting to the below statement, mentioned in online manual ? "the soft-core alpha parameter, a value of 0 results in linear interpolation of the LJ and Coulomb interactions" On Tue, Nov 26, 2013 at 6:35 PM, Justin Lemkul wrote: > On Tue, Nov 26, 2013 at 7:52 AM, bipin singh wrote: > > > Hello, > > > > Below is the text taken from the page number 97 of Gromacs 4.6.4 manual: > > > > "When soft core potentials are selected *(by setting sc-alpha ¿ 0)*, and > > the Coulomb and Lennard-Jones potentials are turned on or off > sequentially, > > then the Coulombic interaction is turned off linearly, rather than using > > soft core interactions, which should be less statistically noisy in most > > cases". > > > > *Doubt:* > > > > > > > > > > *sc-alpha ¿ 0 is actually sc-alpha=0 * > > Am I right ? > > > > > No. The bogus character should indicate "not equal to." > > -Justin > > -- > > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > == > -- > 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. > -- *---Thanks and Regards,Bipin Singh* -- 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] Regarding soft-core potential
Hello, Below is the text taken from the page number 97 of Gromacs 4.6.4 manual: "When soft core potentials are selected *(by setting sc-alpha ¿ 0)*, and the Coulomb and Lennard-Jones potentials are turned on or off sequentially, then the Coulombic interaction is turned off linearly, rather than using soft core interactions, which should be less statistically noisy in most cases". *Doubt:* *sc-alpha ¿ 0 is actually sc-alpha=0 * Am I right ? -- *---Thanks and Regards,Bipin Singh* -- 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] Grompp error while using dual topology for free energy
Thanks Dr. Justin for the reply. I have figure out the problem. On Fri, Nov 22, 2013 at 2:59 AM, Justin Lemkul wrote: > On Thu, Nov 21, 2013 at 4:27 PM, bipin singh wrote: > > > Hi all, > > > > For calculating the free energy of solvation, I have defined the end > states > > in the topology file. But while executing grompp, it displays the error: > > > > Program grompp_mpi, VERSION 4.6.3 > > Source code file: /sw/source/sandbox/gromacs-4.6.3/src/kernel/grompp.c, > > line: 518 > > > > Fatal error: > > No molecules were defined in the system > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > > > > > > > *mdp settings for free energy:* > > > > free-energy = yes > > sc-alpha = 0 > > sc-power = 1 > > sc-r-power = 6 > > init-lambda-state= 0 > > fep-lambdas = 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 > 1.0 > > coul-lambdas = 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 > 1.0 > > nstdhdl = 100 > > dhdl-print-energy= yes > > > > > You forgot the couple-moltype keyword, so grompp has no idea what you're > transforming. > > -Justin > > -- > > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > == > -- > 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. > -- *---Thanks and Regards,Bipin Singh* -- 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] Grompp error while using dual topology for free energy
Hi all, For calculating the free energy of solvation, I have defined the end states in the topology file. But while executing grompp, it displays the error: Program grompp_mpi, VERSION 4.6.3 Source code file: /sw/source/sandbox/gromacs-4.6.3/src/kernel/grompp.c, line: 518 Fatal error: No molecules were defined in the system For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors *mdp settings for free energy:* free-energy = yes sc-alpha = 0 sc-power = 1 sc-r-power = 6 init-lambda-state= 0 fep-lambdas = 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 coul-lambdas = 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 nstdhdl = 100 dhdl-print-energy= yes -- *---Thanks and Regards,Bipin Singh* -- 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.
