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 <ayesha_coms...@hotmail.com> 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 m.eb...@umontreal.ca 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 nguy...@wittenberg.edu 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 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 nguy...@wittenberg.edu: 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 gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of asaffa...@post.tau.ac.il 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 nguy...@wittenberg.edu: 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 posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe
Re: [gmx-users] 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 mark.j.abra...@gmail.com wrote: Hi, On Thu, May 28, 2015 at 5:23 PM bipin singh bipinel...@gmail.com 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 iitd...@gmail.com 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 bipinel...@gmail.com 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 hoemb...@brandeis.edu 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
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 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 kapoorpratib...@gmail.com 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
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 kapoorpratib...@gmail.com 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 kapoorpratib...@gmail.com 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.
[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.
[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] 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 jalem...@vt.edu 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.
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 mikhailyusta...@gmail.com 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 namitasingh9...@gmail.com 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 nm...@york.ac.uk 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 mark.j.abra...@gmail.com wrote: Have you read and followed gmx do_dssp -h? Mark On Mon, Aug 25, 2014 at 2:21 PM, Nikolaos Michelarakis nm...@york.ac.uk 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 use the precompiled dssp executables. *Thanks and Regards,Bipin Singh* On Mon, Aug 25, 2014 at 5:31 AM, Nikolaos Michelarakis nm...@york.ac.uk 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] 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 nm...@york.ac.uk 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] 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 michael.car...@icr.ac.uk 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] 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] 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 ashi.rajpu...@gmail.comwrote: 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) gaurav.saraf.bc...@itbhu.ac.in 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 s...@iacs.res.in 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 jalem...@vt.edu 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.
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 mark.j.abra...@gmail.comwrote: On Sat, Feb 1, 2014 at 8:15 AM, bipin singh bipinel...@gmail.com 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.
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 m.oz...@umiami.edu 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 bipinel...@gmail.com 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 m.oz...@umiami.edu 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 16 opls_270 77GLUHE2 5 0.45 1.008 17 opls_271 77GLU C 60.7 12.011 opls_2710.7 12.011 18 opls_272 77GLU O1 6 -0.815.9994 opls_272 -0.8 15.9994 19 opls_272 77GLU O2 6 -0.815.9994 opls_272 -0.8 15.9994 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 5 7 1 517 1 7 8 1 7 9 1 710 1 10
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 jalem...@vt.edu 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 m.oz...@umiami.edu 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 bipinel...@gmail.com 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 m.oz...@umiami.edu 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 16 opls_270 77GLUHE2 5 0.45 1.008 17 opls_271 77GLU C 60.7 12.011 opls_2710.7 12.011 18 opls_272 77GLU O1 6 -0.8
Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...
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 bipinel...@gmail.com 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 m.oz...@umiami.edu 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
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 suhani.nag...@gmail.comwrote: 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 bipinel...@gmail.com 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 suhani.nag...@gmail.com 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 bipinel...@gmail.com 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 jalem...@vt.edu 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_Listbefore 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 == -- 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. -- *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. -- Rajat Desikan (Ph.D
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 suhani.nag...@gmail.comwrote: 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 jalem...@vt.edu 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
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 nidhijat...@bic-svc.ac.inwrote: 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 ckut...@gwdg.de 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, dxl...@hotmail.com wrote: Ｉ have the same question， too！ At 2013-12-16 22:48:06,Arunima Shilpi writetoas...@gmail.com 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.
[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 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] Regarding Gromacs 5.0 Beta1 release
Thank You Prof. Shirts for your clarification. On Mon, Dec 9, 2013 at 9:40 PM, Michael Shirts mrshi...@gmail.com 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 bipinel...@gmail.com 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.
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 vsha...@imtech.res.in 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 mrshi...@gmail.com wrote: The fluctuation is often of the order of magnitude of dh/dl itself. It's dh/dl that matters. On Thu, Nov 28, 2013 at 1:26 PM, bipin singh bipinel...@gmail.com 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 mrshi...@gmail.com wrote: It's very possible that this is entirely physical. dh/dl fluctuates a lot. You may want to look at graphs of dh/dl after a few 10's of ps to see if it looks reasonable. On Thu, Nov 28, 2013 at 10:04 AM, bipin singh bipinel...@gmail.com 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 bipinel...@gmail.com 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 mrshi...@gmail.com wrote: Define large fluctuations. They might be physical large fluctuations! On Thu, Nov 28, 2013 at 1:19 AM, bipin singh bipinel...@gmail.com 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. -- 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. -- *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. -- 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
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 mrshi...@gmail.com wrote: Define large fluctuations. They might be physical large fluctuations! On Thu, Nov 28, 2013 at 1:19 AM, bipin singh bipinel...@gmail.com 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.
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 bipinel...@gmail.com 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 mrshi...@gmail.comwrote: Define large fluctuations. They might be physical large fluctuations! On Thu, Nov 28, 2013 at 1:19 AM, bipin singh bipinel...@gmail.com 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 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 mrshi...@gmail.com wrote: It's very possible that this is entirely physical. dh/dl fluctuates a lot. You may want to look at graphs of dh/dl after a few 10's of ps to see if it looks reasonable. On Thu, Nov 28, 2013 at 10:04 AM, bipin singh bipinel...@gmail.com 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 bipinel...@gmail.com 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 mrshi...@gmail.com wrote: Define large fluctuations. They might be physical large fluctuations! On Thu, Nov 28, 2013 at 1:19 AM, bipin singh bipinel...@gmail.com 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. -- 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. -- 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
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 pall.szil...@gmail.comwrote: On Wed, Nov 27, 2013 at 3:27 AM, bipin singh bipinel...@gmail.com 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] 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.
