[gmx-users] Help about g_hbond and angle cutoff

Hi gromacs Users: I have a doubt respect to how g_hbond consider the cutoff angle (-a) Acceptor-Donnor-Hydrogen in gromacs 4.5.4. I need to evaluate the hydrogen bonds with an anble larger than 135°. The default value of the angle is cutoff in g_hbond is 30°, so this value means that the H.

Re: [gmx-users] Help about g_hbond and angle cutoff

alejandro esteban blanco munoz wrote: Hi gromacs Users: I have a doubt respect to how g_hbond consider the cutoff angle (-a) Acceptor-Donnor-Hydrogen in gromacs 4.5.4. I need to evaluate the hydrogen bonds with an anble larger than 135°. The default value of the angle is cutoff in g_hbond

[gmx-users] Ligand-ligand Tutorial

Hi, Anyone know any ligand- ligand tutorial? I've been trying to set up a taurine  simulation with lysophosphatidylcholines (LPC) with no success. Thanks in Advance-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] Ligand-ligand Tutorial

Hovakim Grabski wrote: Hi, Anyone know any ligand- ligand tutorial? If there is no receptor, then there is no ligand ;) I've been trying to set up a taurine simulation with lysophosphatidylcholines (LPC) with no success. Without a description of what you've tried, what hasn't worked,

[gmx-users] position restrain

Dear GMX users, I am working on lipid_drg system my drug molecule has 23 atoms. [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CAA 1 -0.073 15.0350 2 CH2 1 DRG CAH 2

Re: [gmx-users] position restrain

Justin A. Lemkul wrote: parto haghighi wrote: Dear GMX users, I am working on lipid_drg system my drug molecule has 23 atoms. [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CAA 1 -0.073

[gmx-users] Simulating multiple fragments

Hi all I was wondering if some body has done simulating multiple copies of small lead like fragments in a solvated box . I want to soak my proteins with multiple copies of diverse fragments along with water as iam interested in finding the hot spots in proteins that can be successfully

[gmx-users] How to the define the A and B states for the calculation of free energy

Hi gromacs-users, I have carefully checked the manual about the define the A and B states for the calcualtion of free energy. And I also known that couple-moltype“ and couple-lambda0 and couple-lambda1. However I have two types of molecules for decoupling in the simulaiton. It seems that

Re: [gmx-users] How to the define the A and B states for the calculation of free energy

xu zhijun wrote: Hi gromacs-users, I have carefully checked the manual about the define the A and B states for the calcualtion of free energy. And I also known that couple-moltype“ and couple-lambda0 and couple-lambda1. However I have two types of molecules for decoupling in the simulaiton.

Re: [gmx-users] How to the define the A and B states for the calculation of free energy

xu zhijun wrote: Thanks Justin. You mean I put the na+ and Ca+ in the same moleculetype？ But I just worry about whether it is feasible to put the two ions in the same moleculetypes even if they have no any connects between them (bond, angle). The chemical definition of a molecule and

Re: [gmx-users] How to the define the A and B states for the calculation of free energy

Thanks a lot Justin. Have a good night. PS: the gromacs tutorials in your home page are really pretty good. --- On Sat, 1/14/12, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] How to the define the A and B states for the calculation