[gmx-users] Need help for the free energy calculation.
Dear all, I am doing the free energy calculation using Gromacs 4.6.4 now. However, I got the message by g_bar: --- Program g_bar, VERSION 4.6.4 Source code file: /home/rui/Downloads/gromacs-4.6.4/src/tools/gmx_bar.c, line: 1208 Fatal error: Could not find a set for foreign lambda = 0.00 in the files for lambda = 0.00 - Could anyone help me to resolve this problem. Please also see my mdp input: --- ; Run control integrator = sd ; Parameters describing what to do, when to stop and what to save nsteps= 500; Maximum number of (minimization) steps to perform 12000ns dt = 0.002 ; 2fs ; Output control cutoff-scheme= group nstlog = 100 nstenergy= 10 nstcalcenergy = 10 ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ns_type = grid pbc = xyz rlist= 1.2 ; Electrostatics coulombtype = PME rcoulomb = 1.2 ; van der Waals vdw-type = cut-off ;rvdw-switch = 0.9 rvdw = 1.2 ;vdw-modifier=Potential-shift-Verlet ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ;Temperature coupling tcoupl=V-rescale ;berendsen tc_grps=Protein CA2+_Water_and_ions tau_t=0.1 0.1;ps time constant for coupling for each group ref_t=300 300;K reference temperature ; Pressure coupling pcoupl = Parrinello-Rahman Pcoupltype=isotropic tau_p=0.5 ref_p=1.0 compressibility=4.5e-5 refcoord_scaling=com ; Free energy control stuff free_energy = yes init_lambda = 0.1 init-lambda-state = -1 delta_lambda = 0 fep-lambdas = 0 0.2 ;coul-laambdas couple-intramol = yes sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 nstdhdl = 10 ; Generate velocities to start gen_vel = no ; Type of constraint algorithm constraints = h-bonds constraint-algorithm = lincs continuation = yes ld_seed =-1 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 ; Output control nstxout = 1000 ; frequency to write coordinates to output trajectory file ;energygrps= Protein; Which energy group(s) to write to disk Thank you very much for any help! Sincerely, Rui Zhang -- Dr. Rui Zhang Postdoctoral Research Associate Department of Veterinary Pathobiology Texas AM University College Station, TX 77840 rzhan...@tamu.edu (305) 301-7879 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't 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] Density profile for COM of residues
Dear All users, I want to calculate the number density profile for COM of my residues. They are located on a surface. Are there any options for counting COMs respect to that surface? -- Sincerely Ali Alizadeh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't 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] radial distribution function of fullerene COM and O of water
On Dec 29, 2013 8:51 PM, mali 18crow...@gmail.com wrote: Hi friends Have performed simulation of fullerene and water molecules and calculated free energy of solvation. Now want to calculate the radial distribution function of fullerene COM and O of water molecules. Could you please help how to perform it. Thanks in advance Mali -- View this message in context: http://gromacs.5086.x6.nabble.com/radial-distribution-function-of-fullerene-COM-and-O-of-water-tp5013563.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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't 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] Why some dihedrals have multiple parameters
Hi friends I have been building a topology and I found that some dihedrals have multiple parameters. Can someone tell me why is that? I imagine they should be used when you need to account for multiple terms in a Fourier representation, but I'm about to write a report and I'm not quite sure now. Thanks in advance. Regards. -- View this message in context: http://gromacs.5086.x6.nabble.com/Why-some-dihedrals-have-multiple-parameters-tp5013574.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.
[gmx-users] Density profile for COM of residues,
Dear All users, I want to calculate the number density profile for COM of my residues. They are located on a surface. Are there any options for counting COMs respect to that surface? -- Sincerely Ali Alizadeh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't 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] radial distribution function of fullerene COM and O of water
first run make_ndx to make an index file of water O atom. Next run g_rdf with -com option. this will give you the R.D.F of com of c60 and water O atom. On Mon, Dec 30, 2013 at 10:43 PM, Pratiti Bhadra pratiti.bha...@gmail.comwrote: On Dec 29, 2013 8:51 PM, mali 18crow...@gmail.com wrote: Hi friends Have performed simulation of fullerene and water molecules and calculated free energy of solvation. Now want to calculate the radial distribution function of fullerene COM and O of water molecules. Could you please help how to perform it. Thanks in advance Mali -- View this message in context: http://gromacs.5086.x6.nabble.com/radial-distribution-function-of-fullerene-COM-and-O-of-water-tp5013563.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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't 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. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't 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] Density profile for COM of residues,
Dlpoy or gromacs? Sent from Yahoo! Mail on Android -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't 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.
