Dear all, any other suggestions on how to operate with g_hbond in order to allow convergence of the autocorrelation function (see message below)?
Moreover, I have another question. On the same trajectories, I'm using g_hbonds also to infer the contacts between the protein and the ligand (and possibly infer van der Waals interactions). This is the command I used: g_hbond -f protein-GLA_mdC.xtc -s protein-GLA_md.tpr -g protein-GLA_md_vdw.log -contact -r 1.4 -num protein-GLA_md_vdwnum.xvg The printout of the command is: Select a group: 1 Selected 1: 'Protein' Select a group: 15 Selected 15: 'GLA' Checking for overlap in atoms between Protein and GLA Calculating contacts between Protein (5935 atoms) and GLA (24 atoms) Found 24 donors and 5935 acceptors Making hbmap structure...done. Reading frame 0 time 0.000 Will do grid-seach on 6x6x4 grid, rcut=1.4 Last frame 3000 time 30000.000 Found 38017 different contacts in trajectory Found 0 different atom-pairs within hydrogen bonding distance Average number of contacts per timeframe 0.000 out of 71220 possible However, the .log file gives me a list of interactions such as: # Donor Hydrogen Acceptor GLA395O4 PRO35O GLA395O4 GLY36N GLA395O4 GLY36CA GLA395O4 GLY36HA1 GLA395O4 GLY36HA2 GLA395O4 GLY36C GLA395O4 GLY36O GLA395O4 ARG37N GLA395O4 ARG37H .................................................................... Moreover, I found previously several hBonds in this trajectory, therefore, I don't understand why the printout tells "Found 0 different atom-pairs within hydrogen bonding distance" and "Average number of contacts per timeframe 0.000 out of 71220 possible". I also used flag -r2 instead of -r, but the result is the same. Maybe this is a trivial question, but...what is the correct way to use the flags -contact and -r (or -r2) within g_hbond command? Thanks a lot Anna Message: 1 Date: Tue, 11 Oct 2011 10:25:32 -0400 From: "Justin A. Lemkul" <jalem...@vt.edu> Subject: Re: [gmx-users] H-bond lifetime with g_hbond To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <4e9451dc.6010...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: > Dear gmx-users, > I have a protein with 5 different ligands. For each system I made 30ns > simulation and I calculated the lifetime of the H-bonds between protein > and ligand with the command: > > g_hbond -f traj.xtc -s topol.tpr -hbm hbmap.xpm -hbn hbond.ndx -ac > hbac.xvg -life hblife.xvg > > During all calculations, the printout of the command gave the same warning: > > > > WARNING: Correlation function is probably not long enough > > because the standard deviation in the tail of C(t) > 0.001 > > > > and as a matter of fact, the tail of C(t) (average C(t) over second half > of acf) reported below this warning was always > 0.001, generally > comprised between 0.45 and 0.74 with two exceptions: a value of > 0.02+/-0.03 and a value of 0.04+/-0.01. > The warning doesn't complain about the value of C(t), it is telling you that the standard deviation in the value is unacceptable. > Therefore, I'm asking if the forward values considered as lifetimes are > reliable or not, and in case, what can I do to avoid this warning. > I can't directly comment on this, but it would seems as if the values are not adequately converged. -Justin > > > Thank you very much and best regards > > Anna > > > ____________________________________________________ > Anna Marabotti, Ph.D. > Laboratory of Bioinformatics and Computational Biology > Institute of Food Science, CNR > Via Roma, 64 > 83100 Avellino (Italy) > Phone: +39 0825 299651 > Fax: +39 0825 781585 > Email: anna.marabo...@isa.cnr.it <mailto:anna.marabo...@isa.cnr.it> > Skype account: annam1972 > Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm > > "When a man with a gun meets a man with a pen, the man with a gun is a > dead man" > (Roberto Benigni, about Roberto Saviano) > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
