[gmx-users] Some problem about the process of calculating MM-PBSA binding free energy

2017-07-20 Thread 刘玉杰
Dear all user; I met some problem when I calculated the binding free energy between protein and ligand by the g_mmpbsa program. I am sure that I had read the tutorials of its official website and some other related information, but I don’t know what should I set the value of pconc or nconc in the

[gmx-users] NEMD with sinusoidal pressure variation

2017-07-20 Thread Aarushi Bhargava
I am simulating a protein using gromacs 5.0.2 and want to apply time varying pressure (preferably sine wave) on it. How should I do it in NEMD? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

Re: [gmx-users] Computing free energy differences from the dH/dl values directly

2017-07-20 Thread Miguel Caro
I think the mail server messed up the latex formulas, hopefully this is displayed better: Hello, I want to do thermodynamic integration directly from the ∂H/∂λ values in the md.xvg files, rather than using gmx bar, because I want to do several manipulations (eventually). On the tutorial on solvat

Re: [gmx-users] pdb2gmx

2017-07-20 Thread Peter Stern
Is your first residue GLY-12? If so you have exactly 368 residues in your protein: 12-379 Peter -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of ?farial tavakoli? ?? Sent: Thursday, July 20

[gmx-users] Drude force field

2017-07-20 Thread Shraddha Parate
Hi gmx users! For polarizable effect, I was setting drude force field in Gromacs I attempted running Lagrangian Dynamics simulation using Drude force field. mdp file format was used from the supporting data in below paper. [2015] Implementation of extended Lagrangian dynamics in GROMACS for polar

[gmx-users] pdb2gmx

2017-07-20 Thread ‪farial tavakoli‬ ‪
Hello  I want to create a .gro and .top file from my protein that contains 379 aminoacids in it's .pdb file by using gromos96 54a7 force field: pdb2gmx -f protein.pdb -o protein.gro -water spce -ignh but when gro and topology files are created , I see that message: Start terminus GLY-12: GLY-NH3+

[gmx-users] Computing free energy differences from the dH/dl values directly

2017-07-20 Thread Miguel Caro
Hello, I want to do thermodynamic integration directly from the ∂H/∂λ\partial H / \partial \lambda values in the md.xvg files, rather than using gmx bar, because I want to do several manipulations (eventually). On the tutorial on solvated methane how to use gmx bar is explained, however this is a

Re: [gmx-users] dihedral restraint

2017-07-20 Thread Yu Ogawa
Hi Gangotri, You can increase the force constant. Best, -Yu 2017-07-19 19:15 GMT+01:00 gangotri dey : > Hello all, > > I am a relatively new user of gromacs. Hence, I am encountering some > problem. > > I am studying few drug molecules onto a metal oxide surface. I would like > to constrain the R

Re: [gmx-users] Ethanol energies with CHARMM ff

2017-07-20 Thread Sonia Milena Aguilera Segura
>On 7/18/17 1:28 PM, Sonia Milena Aguilera Segura wrote: >> Dear GROMACS users, >> >> I am running a 4 nm box of ethanol and once I finished the MD, I got the >> right T, P, density. However, I noticed that my energies are odd. After >> several trials with different parameters and box sizes I >>

[gmx-users] pull COM "geometry = direction periodic" problem

2017-07-20 Thread edesantis
dear all, I am studying the affinity between an antibody and an amyloid peptide; I am interested in the evaluation of the PMF. I tried to preform the COM pulling simulation using the "pull-geometry = direction", but for same the configurations (the ones in which the COMs of the two groups are