Re: [gmx-users] ignoring -h atoms

Dear Maria, I’m not saying that it never makes a difference for the topology generation, but it depends on the quality of your input structure. Justin and I both gave examples of why you might want to use it. When you do, -ignh ignores the hydrogens in the input pdb and uses the rtp to model

[gmx-users] ignoring -h atoms

Dear ERIK.. """..No. -ignh ignores the hydrogen atoms in the input structure, but uses the rtp file(s) to generate new hydrogens. This is useful, for example, when some hydrogens are missing in the pdb file. The structure and topology will therefore contain hydrogens in the end also with

Re: [gmx-users] Ignoring H-atoms.

On 2/7/17 3:42 AM, Amir Zeb wrote: Thanks Erik, I got the explanation you kindly posted regarding the posted discussion. I would like to extend the question that if some one does not flag the -ignh, so does it mean that the input H-atoms are still there and the force field will consider them

Re: [gmx-users] Ignoring H-atoms.

Thanks Erik, I got the explanation you kindly posted regarding the posted discussion. I would like to extend the question that if some one does not flag the -ignh, so does it mean that the input H-atoms are still there and the force field will consider them during the rtp file generation?

Re: [gmx-users] Ignoring H-atoms.

> On 7 Feb 2017, at 08:35, Amir Zeb wrote: > > Hello Maria, > > f igoring h-atom command is applied ,,then forcefield will ignore all the > added h-atoms > > What I know about -ignh flag, it does not mean to remove the h-atoms, > alternatively means that during the

Re: [gmx-users] Ignoring H-atoms.

Hello Maria, f igoring h-atom command is applied ,,then forcefield will ignore all the added h-atoms What I know about -ignh flag, it does not mean to remove the h-atoms, alternatively means that during the topology generation, the force field is considering the h-atoms as the light atoms and

[gmx-users] Ignoring H-atoms.

Dear Gromacs users,, if igoring h-atom command is applied ,,then forcefield will ignore all the added h-atoms,,,so my question is then it would be a vaccum simulation if the h-atom will be ignored,,secondly the results will be also differnt then when h-atoms are considered. Regards.. -- Gromacs