Re: [gmx-users] PMF trails off to infinity.

2012-07-03 Thread Justin A. Lemkul
l_fig.jpg >>> >>> >>> >>> -Original Message- >>> From:gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On >>> Behalf Of Justin A. Lemkul >>> Sent: Monday, July 02, 2012 3:56 PM >>> To: Discussion

Re: [gmx-users] PMF trails off to infinity.

2012-07-02 Thread Justin A. Lemkul
On 7/2/12 4:51 PM, Laura Kingsley wrote: Basically what I'm doing is pulling a ligand out of a protein towards a dummy atom, which has a mass of 1 and no charge. I've attached the a portion .mdp files for both the smd portion and the umbrella sampling. I know that the ligand gets very close pos

Re: [gmx-users] PMF trails off to infinity.

2012-07-02 Thread Laura Kingsley
64.photobucket.com/albums/u370/laurakingsley/?action=view¤t=pull_fig.jpg -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Monday, July 02, 2012 3:56 PM To: Discussion list for GROMACS users Subject: Re:

Re: [gmx-users] PMF trails off to infinity.

2012-07-02 Thread Justin A. Lemkul
Discussion list for GROMACS users Subject: Re: [gmx-users] PMF trails off to infinity. On 7/2/12 3:53 PM, Laura Kingsley wrote: Basically what I'm doing is pulling a ligand toward a dummy atom. I pull the ligand until its COM is very close (a few angstroms) from the dummy atom. Could this

Re: [gmx-users] PMF trails off to infinity.

2012-07-02 Thread Laura Kingsley
=pull_fig.jpg -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Monday, July 02, 2012 3:56 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] PMF trails off to infinity. On 7/2/12 3:53 PM, Laura

RE: [gmx-users] PMF trails off to infinity.

2012-07-02 Thread Kingsley, Laura J
, July 02, 2012 3:56 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] PMF trails off to infinity. On 7/2/12 3:53 PM, Laura Kingsley wrote: > Basically what I'm doing is pulling a ligand toward a dummy atom. I pull the > ligand until its COM is very close (a few angstrom

Re: [gmx-users] PMF trails off to infinity.

2012-07-02 Thread Justin A. Lemkul
On 7/2/12 3:53 PM, Laura Kingsley wrote: Basically what I'm doing is pulling a ligand toward a dummy atom. I pull the ligand until its COM is very close (a few angstroms) from the dummy atom. Could this be causing this behavior? What information would help? I'm having a tough Collisions betwe

Re: [gmx-users] PMF trails off to infinity.

2012-07-02 Thread Laura Kingsley
Basically what I'm doing is pulling a ligand toward a dummy atom. I pull the ligand until its COM is very close (a few angstroms) from the dummy atom. Could this be causing this behavior? What information would help? I'm having a tough time getting the figures attached but may be I could email

Re: [gmx-users] PMF trails off to infinity.

2012-07-02 Thread Justin A. Lemkul
On 7/2/12 9:54 AM, Laura Kingsley wrote: Hello, I am using steered MD and umbrella sampling to generate a PMF profile for pulling a small ligand 3 nm. As I pull the ligand from 3A toward 0 A, the PMF starts a dramatic uphill climb. This does not agree with the force profile which seems to le