Re: [gmx-users] PMF of ligand transport

Aswathy wrote: On Mon, May 17, 2010 at 12:14 PM, Aswathy > wrote: Hi, I tried to calculate PMF for the ligand transport using pull_geometry=position. Let me explain you what I did so far, I picked a small collection of backbone atoms nearly

Re: [gmx-users] PMF of ligand transport

On Mon, May 17, 2010 at 12:14 PM, Aswathy wrote: > Hi, > > I tried to calculate PMF for the ligand transport using > pull_geometry=position. > > Let me explain you what I did so far, > > I picked a small collection of backbone atoms nearly from the centre of the > channel.My SMD was displacing th

Re: [gmx-users] PMF of ligand transport

Hi, I tried to calculate PMF for the ligand transport using pull_geometry=position. Let me explain you what I did so far, I picked a small collection of backbone atoms nearly from the centre of the channel.My SMD was displacing the ligand from extracellular to intracellular. I checked the pullx

Re: [gmx-users] PMF of ligand transport

Chris, I understand, Sorry for that . Actually I mixed up the concept of SteeredMd with umbrella sampling. So I was confused whenever you people gave suggestions. Now I thing I got the idea , Thanks for you people. I will try myself and see. Thanks once again. -Aswathy On Tue, May 11, 2010 at

[gmx-users] PMF of ligand transport

It represents a difference in coordinate space. You'll get the most out of this list if you continue to try to solve your problems before posting and avoid submitting every question/problem that you hit upon under a continuously in-use title. Did you try it and look at you -px output file?

Re: [gmx-users] PMF of ligand transport

Hi Chris, Thank you very much for your detailed mail. Now I have a doubt on this pull_init parameter. i read your previous posts regarding this, but still have a confusion. My query is that for each configuration when I run umbrella sampling, will this pull_init value needs to change?(I suppose

[gmx-users] PMF of ligand transport

Pick a small collection of backbone atoms near the center of your channel and use them as your reference group. Overcome the sign problem by optimal selection of pull options (see below). pull_pbcatom values should not be important if you select your groups as I suggest -- otherwise be sure to un

[gmx-users] PMF of ligand transport

Don't use a dummy particle for your PMF if you can avoid it and test it thoroughly if you must use it. In my own work, I have received what appears to be erroneous results when using a dummy atoms together with dihedral restraints and the pull code. In my case I was actually using a dummy atom

Re: [gmx-users] PMF of ligand transport

Aswathy wrote: Thank you very much for all replies. No w I just want to try SMd with geometry type as position . But one thing is still confusing me, ie; reference group. If you have already generated a suitable set of positions from which you have generated umbrella sampling windows, y

Re: [gmx-users] PMF of ligand transport

Using a flexible reference to generate a PMF is certainly not a good idea. More than affecting your convergence, your distance may have only little to do with the actual position of your ion in the channel. Imagine the ion is in a stable position and has to go over some energy barrier. It l

[gmx-users] PMF of ligand transport

Dear Aswathy: While not technically incorrect, it will make convergence much more difficult and is probably realistically incorrect given today's cpu power. But then again perhaps you have some particularly important reason to make that choice. In the absence of that, find some atom(s) th

Re: [gmx-users] PMF of ligand transport

Aswathy wrote: On Mon, May 10, 2010 at 6:29 PM, Justin A. Lemkul > wrote: Ok . Now I understood. I have one more doubt , as I mentioned to you, I am using one residue in the extracellular loop as a reference point. Since this is in the loop, do you think

Re: [gmx-users] PMF of ligand transport

On Mon, May 10, 2010 at 6:29 PM, Justin A. Lemkul wrote: > Ok . Now I understood. I have one more doubt , as I mentioned to you, I am > using one residue in the extracellular loop as a reference point. Since this > is in the loop, do you think it can be good reference point (due to th large > flu

Re: [gmx-users] PMF of ligand transport

Aswathy wrote: I am pulling through the channel with respect to a single residue on one "side"(extracellular) of the structure. I have used pull_geometry = distance & pull_dim = N N Y. From this what I understood is ligand will pull along the z direction with respect to the reference group

Re: [gmx-users] PMF of ligand transport

I am pulling through the channel with respect to a single residue on one "side"(extracellular) of the structure. I have used pull_geometry = distance & pull_dim = N N Y. From this what I understood is ligand will pull along the z direction with respect to the reference group (away from r_57). (i

Re: [gmx-users] PMF of ligand transport

Aswathy wrote: Thanks for your reply. In this case reference (r57) is not the part of the channel. But it is a residue in the loop above the channel entry. Thats why I used pull_geometry=distance. Therefore I am pulling the ligand away from this reference. So you are not pulling throu

Re: [gmx-users] PMF of ligand transport

Thanks for your reply. In this case reference (r57) is not the part of the channel. But it is a residue in the loop above the channel entry. Thats why I used pull_geometry=distance. Therefore I am pulling the ligand away from this reference. Thanks -Aswathy On Mon, May 10, 2010 at 3:05 PM, Tho

Re: [gmx-users] PMF of ligand transport

Hi, If you defined the reference (r_57) as part of your channel then with pull_geometry=distance you will have problems as the distance between pull_group1 and pull_group0 becomes closer to zero and then the distance becomes positive again. I recently had this with my umbrella sampling simul

Re: [gmx-users] PMF of ligand transport

Can any one help me please? I looking forward to hear from any of you. Thank you. On Thu, May 6, 2010 at 1:19 PM, Aswathy wrote: > Ok i will explain you in detail. > > Initially i pulled the ligand through the protein channel , using the > given parameters. > > pull = umbre

Re: [gmx-users] PMF of ligand transport

Ok i will explain you in detail. Initially i pulled the ligand through the protein channel , using the given parameters. pull = umbrella pull_geometry= distance pull_dim = N N Y pull_start = yes pull_nstxout = 10 pull_ns

Re: [gmx-users] PMF of ligand transport

Aswathy wrote: Hi gromacs users, I am using Gromacs 4.0.4 package. I am doing SMD of a ligand transport through a channel. I performed SMD and did umbrella sampling (Thanks to Justin for his tutorial). Extracted frames with a window spacing interval of ~0.12nm. and did 1ns sampling. Hist

[gmx-users] PMF of ligand transport

Hi gromacs users, I am using Gromacs 4.0.4 package. I am doing SMD of a ligand transport through a channel. I performed SMD and did umbrella sampling (Thanks to Justin for his tutorial). Extracted frames with a window spacing interval of ~0.12nm. and did 1ns sampling. Histograms are with reasona