Re: [gmx-users] extra gro file generation

Dear Riccardo Concu and Mirco Wahab, Thanks for your perfect responses. Regards, Sarah -- gmx-users mailing listgmx-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! * Plea

[gmx-users] extra gro file generation

Dear all, I'm going to perform a molecular dynamics simulation on a protein. As a default the simulation gives one final *.gro file. I need to get a .gro file after each say 500 ps of my simulation, in addition of the final file. How can I do so? Best regards, Sarah Keshavarz -- gmx-users mailin

[gmx-users] Re: free energy of system

Dear Justin, Thanks for your response and the perfect tutorial. I found the details I needed in it. Best regards, Sarah -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Li

[gmx-users] free energy of system

Dear all, I'm interested in calculating the Gibbs free energy of some systems. I have several questions in this regard: 1- The g_energy command gives some values in kJ/mol for total energy and enthalpy. Does the reported total energy include entropy effects? (The calculated total energy and entha

[gmx-users] Re: No molecules were defined in the system/ No such molecule type

> > Dear Justin, > I reeditted my .top and .gro files for drug-complex simulation. Now after "grompp -f em.mdp -c _b4ion.gro -p .top -o _b4ion.tpr" command, the following messages appear and the procedure ends with no .tpr output: Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entr

[gmx-users] No molecules were defined in the system/ No such molecule type Dio

Dear all, I'm trying to simulate several drug-protein complexes on a clustered server. I used PRODRG and editted my .top, .pdb, .gro and posre.itp files. Here is the final lines of my .top file: ; Include Position restraint file ; Include Position restraint file #ifdef POSRES #include "posre

[gmx-users] T-coupling

Dear Gromacs Users, I need to simulate two protein structures by Gromacs 5.4.0. For protein A, the net charge is zero so I don't add any ions. All the commands work properly unitil mdrun of the A_pr.tpr: mdrun -s A_pr.tpr -o A_pr.trr -c A_b4md.gro -g pr.log -e pr.edr& ==> the error: too many LINC

[gmx-users] Re: Force field parameters for phosphorylated

Dear Bharat, You can use the Dundee PRODRG server to prepare the topology/parameter of any structure for GROMACS or some other programs. Here is the link: http://davapc1.bioch.dundee.ac.uk/prodrg/ you should tag the phosphate group and draw the structure of phosphotyrosine and load it. Good Luck

[gmx-users] coordination file

it. Is it really my problem? Can someone explain how I can generate a pre-equilibrated coordination file similar to spc216.gro but with nitrogen? Thanks. Cheers, Sarah K. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search t

[gmx-users] tip5p.gro

Dear Justin, I found out that as you had said, my naming wasn't consistent. I checked and manipulated all file in share/top. i didn't have any problem with files flexwaterguson.itp, atommass.dat, spc.itp, spce.itp, spc216.gro and tip3.itp but when it comes to files tip4p.gro and tip5p.gro I hang.

[gmx-users] molecule type

imulate in non-aqous condition? Cheers, Sarah K. -- gmx-users mailing listgmx-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

[gmx-users] Re: invalid line (coordinates)

dear Justin, The link of (http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology) helped but still I have problem. There are 35344SOL molecules in my _solv.gro file. the last atom is N2 72342. The last part of my topol.top file is: [molecules

[gmx-users] Re: invalid line

dear Justin A. Lemkul, thanks for your reply. You were right. Now, it works and generates the nitrogen box. But when I type: grompp_d -f ions.mdp -c 3INC_solv.gro -p topol.top -o ions.tpr I recieve this error: source file: grompp.c, line: 362 number of coordinates in coordinate file (3INC_solv.gr

[gmx-users] invalid line

dear gromacs users, I'm solvating my protein in nitrogen box. I have changed my spc216.gro, spc.itp and spce.itp files. I face the following error. How can I fix it? invalid line in /usr/share/gromacs/top/spc216.gro for atom 407: 0.41200 0.41200 0.41200 thanks in advance. Best regards,

[gmx-users] zero SOL molecules

Dear all, I am adding Nitrogen box instead of water molecules to my protein. Based on your guidelines I generated the coordination and topology file of nitrogen. Then I used the following command: genbox -cp A_newbox -ci -42000mol N2C.gro -o A_solv.gro -p topol.top N2C.gro is my new file made man

[gmx-users] Re: Nitrogen box

, Sarah Keshavarz > sarah k wrote: >> dear users, >> >> I want to use Nitrogen as my solvent. How can I prepare the box and >> compile the *.gro file? Please, guide me in detail. Thanks in advance! >> > > Make a coordinate file for a single N2 molecule (sh

[gmx-users] Nitrogen box

dear users, I want to use Nitrogen as my solvent. How can I prepare the box and compile the *.gro file? Please, guide me in detail. Thanks in advance! Regards, Fatemeh Keshavarz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search t