Re: [gmx-users] Unknown bond_atomtype when trying to use charm27 with cgenff

On 11/26/16 2:41 PM, Jonathan Phillips wrote: Hi, I'm trying to run a simulation of a protein:ligand complex using chamm27 and cgenff2b7. After a little hacking (I'm using a PRES), I've used charmm2gromacs-pvm.py to convert cgenff2b7 to cgenff2b7.ff/, and then combined that with the charmm27

Re: [gmx-users] The time need for each window in umbrella sampling

Hi, Thanks for the answer! Regards, Farideh On Sat, Nov 26, 2016 at 11:37 PM, Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > block averaging or perhaps reverse cumulative averaging > http://scitation.aip.org/content/aip/journal/jcp/120/6/10.1063/1.1638996 > (though the later will

Re: [gmx-users] Removal of Waters in Hydrophobic Core

I have not run that in a long time, but looking at it (and my initial post here: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2006-May/021526.html ) it seems like I wrote out the instructions incorrectly. Sorry about that! In the post linked above, step 8 is: cat

Re: [gmx-users] The time need for each window in umbrella sampling

block averaging or perhaps reverse cumulative averaging http://scitation.aip.org/content/aip/journal/jcp/120/6/10.1063/1.1638996 (though the later will probably be a pain with PMFs). From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

[gmx-users] Unknown bond_atomtype when trying to use charm27 with cgenff

Hi, I'm trying to run a simulation of a protein:ligand complex using chamm27 and cgenff2b7. After a little hacking (I'm using a PRES), I've used charmm2gromacs-pvm.py to convert cgenff2b7 to cgenff2b7.ff/, and then combined that with the charmm27 forcefield that comes with gromacs. pdb2gmx runs

Re: [gmx-users] setting up a pull vec

Hello Christopher, I have restrained the protein chain and ligand during previous NPT equilibration step(10ns). Is it still possible that the structure will scatter all over if we start pulling ? I want to pull the ligand out of the binding site of this protein and collect intermediary

[gmx-users] LJ wall

Dear Gromacs users , How Can i change lennard-jones wall s location at Z direction ? I use lennard jones wall with these command in mdp file : ... pbc = xy nwall= 2 wall-atomtype = opls_740 opls_740 wall-type = 9-3 wall-density

[gmx-users] The time need for each window in umbrella sampling

Dear Gromacs users, Is there any criteria tk determine tge optimum run time for each window in umbrella sampling? My receptor has equilibrated after 30 ns of MD. Should I consider the same run time for each window? Regards, Farideh -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] topolbuild ( Failing to read oxygen in H2O )

Dear David van der Spoel Thank you for giving me advice. I'll choose TIP4P/Ice model and write its parameters on the topology files. Sincerely. Keisuke Ohki, senior student. Dept. applied physics and physico-informatics., Keio University. -- Gromacs Users mailing list * Please search the

Re: [gmx-users] topolbuild ( Failing to read oxygen in H2O )

On 26/11/16 09:24, 大木啓輔 wrote: Dear gromacs users I have a question why topolbuild fails to read oxygen in H2O. I want to make a topology file of methane hydrate structure with topolbuild and run simulation in gromacs. For these simple molecules you want hand-tuned force fields not

[gmx-users] topolbuild ( Failing to read oxygen in H2O )

Dear gromacs users I have a question why topolbuild fails to read oxygen in H2O. I want to make a topology file of methane hydrate structure with topolbuild and run simulation in gromacs. I used following command line: ./topolbuild -n ../HYDRATE_A -dir ../dat/gromacs -ff oplsaa -purge 0

[gmx-users] The time need fir each window in umbrella sampling

Dear Gromacs users, Is there any criteria tk determine tge optimum run time for each window in umbrella sampling? My receptor has equilibrated after 30 ns of MD. Should I consider the same run time for each window? Regards, Farideh -- Gromacs Users mailing list * Please search the archive at