Re: [gmx-users] trash error in linux

Please ask on a more suitable forum. Searching Google will probably be profitable. Mark On Tue, Jan 6, 2015 at 7:43 AM, mah maz wrote: > Dear all, > > I have encountered a problem much related to linux not Gromacs. I wonder if > anyone has seen this error before : "trash has reached maximum siz

Re: [gmx-users] g_sas problem?

Thanks a lot for the reply. I believe this 122 atoms belong to my ligand. I generate the ligand.itp file by acpype tool and the system was assigned for Amber FF. BTW, why does g_sas ask twice to select a group for output as following? and a group for output: Select a group: 26 Selected 26: 'P

[gmx-users] trash error in linux

Dear all, I have encountered a problem much related to linux not Gromacs. I wonder if anyone has seen this error before : "trash has reached maximum size please clean manually" while it is actually empty. any solutions? thank you! -- Gromacs Users mailing list * Please search the archive at ht

Re: [gmx-users] After solvation and before adding ions, number of molecules does not agree even though number of H2O molecules does

On 1/5/15 5:21 PM, Thomas Lipscomb wrote: Dear gmx-users, I am trying to simulate a Maximin 3 antimicrobial peptide inserted into a membrane. The top of this tutorial page:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/04_ions.html Has this command (th

Re: [gmx-users] g_sas problem?

On 1/5/15 4:01 PM, Albert wrote: Hello: I am interested in the solvent access surface area change after ligand binding to protein. I performed protein/ligand complex MD in Gromacs. I try to obtain SASA with command: g_sas_mpi -f nvt.xtc -nopbc -s nvt-4.tpr -o area.xvg -n Reading frame

Re: [gmx-users] restraint the CM of a molecules in any one of the directions.

On 1/5/15 9:31 AM, Sridhar Kumar Kannam wrote: Hi Justin, Please see Figure 1 of the attached paper. I have a SiN nanopore/membrane with the solvent on both the sides. The protein is inside the pore as in Figure 1a. Let say the pore axis is along the z-axis. I want to constraint the CM of the

Re: [gmx-users] Is the PMF from "gmx wham" a free energy curve?

On 1/5/15 8:52 AM, Alexander Björling wrote: Dear users, I have a question about how to interpret (rather than about how to perform) a GROMACS calculation. I have calculated the Potential of Mean Force for separating two protein chains, in order to estimate the free energy of monomerization f

[gmx-users] After solvation and before adding ions, number of molecules does not agree even though number of H2O molecules does

Dear gmx-users, I am trying to simulate a Maximin 3 antimicrobial peptide inserted into a membrane. The top of this tutorial page:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/04_ions.html Has this command (though I changed the name of system_solv.gro to

Re: [gmx-users] All-atom vs United-atom force fields and hydrogen bonds

Thank you Justin for the detailed and informative response. I’ve now realized that I was using inappropriate parameters for the GROMOS force field and that if I used the recommended cutoffs rvdw =! rc and I could not use the Vartlet scheme. Switching to CHARMM36 and using the recommended cutoffs

Re: [gmx-users] Fwd: Frequency dependent dielectric of water

On 2015-01-05 20:56, Bharat Sharma wrote: Hello Experts, I am interested to calculate frequency dependent dielectric constant. I prepared a dipcorr.xvg file and used g_dielectric function of gromacs to calculate frequency dependent dielectric of water. I used this command. *g_dielectric_mpi -f

[gmx-users] g_sas problem?

Hello: I am interested in the solvent access surface area change after ligand binding to protein. I performed protein/ligand complex MD in Gromacs. I try to obtain SASA with command: g_sas_mpi -f nvt.xtc -nopbc -s nvt-4.tpr -o area.xvg -n Reading frame 0 time0.000 Select a group

Re: [gmx-users] Electrostatic potential

Dear justin, I want to calculated electrostatic potential (dipoles potential), but i don't know what command must be used, would you please help me? this potential must be like this file that attached. Many thanks, Mrs. Mahdavi On Tuesday, January 6, 2015 12:13 AM, asasa qsqs wrote: Dear

[gmx-users] Electrostatic potential

Dear justin, I want to calculated electrostatic potential (dipoles potential), but i don't know what command must be used, would you please help me? Many thanks, Mrs. Mahdavi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_

[gmx-users] Fwd: Frequency dependent dielectric of water

Hello Experts, I am interested to calculate frequency dependent dielectric constant. I prepared a dipcorr.xvg file and used g_dielectric function of gromacs to calculate frequency dependent dielectric of water. I used this command. *g_dielectric_mpi -f dipcorr.xvg -eps0 95 -epsRF 1 -ffn exp_exp -

[gmx-users] Is the PMF from "gmx wham" a free energy curve?

Dear users, I have a question about how to interpret (rather than about how to perform) a GROMACS calculation. I have calculated the Potential of Mean Force for separating two protein chains, in order to estimate the free energy of monomerization for this dimer, loosely following Justin Lemkul's

[gmx-users] Questions about implementing REST in GROMACS 4.6.5

Dear gromacs user: Recently, I am trying to implement Replica Exchange with Solute Tempering in GROMACS following the way proposed by tsuyoshi terakawa(On easy implementation of a variant of the replica exchange with solute tempering in GROMACS, J Comput Chem. 2011 May).I have searched in the gmx-

Re: [gmx-users] How to calculate energy after production MD

On 1/4/15 6:57 PM, Mark Abraham wrote: Hi, You need to define an index group, use it in a new .mdp file as an energy group, and then follow http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy But this will only give short-range nonbonded energies. To get the "energy of the he