Re: [gmx-users] PMF calculation

On 8/19/13 12:27 PM, Za Pour wrote: Dear gmx-users Iwould like to calculate the PMF between two nanotubes covered with some molecules. To do that, one nanotube has to be held fixedly and another one is supposed to be moved as a rigid entity. To generate configurations, for fixed nanotube

[gmx-users] PMF calculation

Dear gmx-users Iwould like to calculate the PMF between two nanotubes covered with some molecules. To do that, one nanotube has to be held fixedly and another one  is supposed to be moved as a rigid entity. To generate configurations,  for fixed nanotube  I used position restraints in all direc

[gmx-users] PMF calculation between protein and ligand

Sir I have query as to how to go ahead for potential mean force (PMF) calculation between protein and ligand. As per the umbrella sampling protocol you have provided us in gromacs tutotrial it says it is for protein molecules... -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scho

[gmx-users] PMF and jacobian correction

Dear Gromacs user,   I was having a question on when need to use jacobian coorection of -2KTln(r) ( gromacs manual chapter 6) term when calculating PMF. I understand for a 3-dimensional radial coordinate like distance between two groups, this term need to taken care of. But, if the PMF is comput

Re: [gmx-users] PMF and Histograms

On 1/28/13 9:00 AM, Steven Neumann wrote: Dear Gmx Users, Dear Justin, I run umbrella samplig with small molecule binding protein. With 11 windows and 0.2 nm spacing I got: PMF: http://speedy.sh/zevcp/profile.JPG Hisotogram: http://speedy.sh/8Cua2/histo.JPG (I used -min and -max options o

RE: [gmx-users] PMF Transmembrane proteins

...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 30 December 2012 20:08 To: Discussion list for GROMACS users Subject: Re: [gmx-users] PMF Transmembrane proteins On 12/30/12 2:57 PM, Nash, Anthony wrote: > Dear Justin > > Thanks for your reply. > > I am studying a TM p

Re: [gmx-users] PMF Transmembrane proteins

On 12/30/12 2:57 PM, Nash, Anthony wrote: Dear Justin Thanks for your reply. I am studying a TM peptide, looking at how favourable the front and reverse face are. Hence, different orientations but the same composition of amino acids. I then have a duplicate of this system (call it system B),

RE: [gmx-users] PMF Transmembrane proteins

to putting up some ASAP. Thanks very much for your help Anthony From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 30 December 2012 19:25 To: Discussion list for GROMACS users Subje

Re: [gmx-users] PMF Transmembrane proteins

On 12/30/12 12:28 PM, Nash, Anthony wrote: Dear gmx users, I posted a couple of weeks ago with regards to correctly using umbrella sampling and the WHAM on atomistic transmembrane proteins with a reaction coordinate as a function of interhelical distance. I have a single TM dimer, but with a d

[gmx-users] PMF Transmembrane proteins

Dear gmx users, I posted a couple of weeks ago with regards to correctly using umbrella sampling and the WHAM on atomistic transmembrane proteins with a reaction coordinate as a function of interhelical distance. I have a single TM dimer, but with a different transmembrane domain face at the he

[gmx-users] PMF - error bars

Dear Gmx Users, I have output from Umbrella Sampling simulations - PMF curve obtained by WHAM. I want to create on the plot error bars. I have 20 windows each corresponding to 80 ns simulation. Shall I create PMF from those results based for 40-60 ns then 60-80 and plot them? Please help. Steven

[gmx-users] PMF - Protein-Me​brane

The large magnitudes of orthogonal barriers in such systems will lead to both systematic and statistical sampling errors that motivate the application of both approaches, preferably repeated a few times each. So I think that Justin is right, in an idealized situation. I might modify his statem

Re: [gmx-users] PMF - Protein-Me​brane

On 8/10/12 11:18 AM, dariush wrote: Hi All, I have a question regards to PMF: Consider we are sure one protein will bind to membrane after 100ns in MD run and make a complex. Instead of pulling protein to membrane to calculate PMF, can we start from last configuration of protein-membrane co

[gmx-users] PMF - Protein-Me​brane

Hi All, I have a question regards to PMF: Consider we are sure one protein will bind to membrane after 100ns in MD run and make a complex. Instead of pulling protein to membrane to calculate PMF, can we start from last configuration of protein-membrane complex and pull out protein to separate

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

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

[gmx-users] PMF trails off to infinity.

/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, J

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

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.

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.

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.

=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.

, 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.

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.

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.

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

[gmx-users] PMF trails off to infinity.

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 level out. Any ideas about what might be go

Re: [gmx-users] PMF profile from Umbrella - Plateau

On Wed, May 16, 2012 at 4:20 PM, Justin A. Lemkul wrote: > > > On 5/16/12 11:16 AM, Steven Neumann wrote: > >> >> >> On Wed, May 16, 2012 at 3:38 PM, Justin A. Lemkul > > wrote: >> >> >> >>On 5/16/12 10:25 AM, Steven Neumann wrote: >> >>Dear Justin, >> >>

Re: [gmx-users] PMF profile from Umbrella - Plateau

On Wed, May 16, 2012 at 3:38 PM, Justin A. Lemkul wrote: > > > On 5/16/12 10:25 AM, Steven Neumann wrote: > >> Dear Justin, >> >> I pulled my ligad away of 6nm from the protein and obtained beautiful and >> smooth >> curve of PMF using 28 windows. Starting from zero kcal/mol corresponding >> to a

Re: [gmx-users] PMF profile from Umbrella - Plateau

On 5/16/12 11:16 AM, Steven Neumann wrote: On Wed, May 16, 2012 at 3:38 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote: On 5/16/12 10:25 AM, Steven Neumann wrote: Dear Justin, I pulled my ligad away of 6nm from the protein and obtained beautiful and smoot

Re: [gmx-users] PMF profile from Umbrella - Plateau

On 5/16/12 10:25 AM, Steven Neumann wrote: Dear Justin, I pulled my ligad away of 6nm from the protein and obtained beautiful and smooth curve of PMF using 28 windows. Starting from zero kcal/mol corresponding to app 0.3 nm then minima and curve increase till my plateau which starts from app 1

[gmx-users] pmf contradicts

Dear colleagues, > I have a problem with PMF calculations with umbrella sampling. A small part of a big molecule migrates from conformation A to conformation B. Although g_wham computes free energy as positive value of ~70kJ/mol for A->B transformation, an average potential energy of the fragm

[gmx-users] PMF curve

Hello, I got a PMF curve like 0...-2...022. its converged at 22. I have a doubt in the final deltaG value, for this curve the deltaG is 22-2 or 22-0. Regards, Vijay. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archi

[gmx-users] PMF curve

Hello, I have done umbrella sampling for 10ns on 23 windows and g_wham program shows converged histograms and PMF curve. I used the following g_wham command, g_wham -it tpr-files.dat -if pullf-files.dat -unit kCal -o profile.xvg -hist histo.xvg -b 1000 -e 1 I considered first 1ns simulation

[gmx-users] PMF with nanotube

Hello, I am trying to find the PMF for the diffusion of small molecule through a nanotube. I have generated the umbrella sampling windows from pull_geometry=direction simulation and umbrella sampling with pull_geometry=position. I guess the PMF for this system can be obtained by combining the g_wh

Re: [gmx-users] PMF when pulling in -Z direction

bars will be as wild as the values in the PMF plot. -Justin Best, nahren *From:* Justin A. Lemkul *To:* nahren manuel ; Discussion list for GROMACS users *Sent:* Friday, November 4, 2011 7:44 PM *Subject:* Re: [gmx-

Re: [gmx-users] PMF when pulling in -Z direction

, approx. 1 ns runs in 5 windows) Best, nahren From: Justin A. Lemkul To: nahren manuel ; Discussion list for GROMACS users Sent: Friday, November 4, 2011 7:44 PM Subject: Re: [gmx-users] PMF when pulling in -Z direction nahren manuel wrote: > Dear Grom

Re: [gmx-users] PMF when pulling in -Z direction

nahren manuel wrote: Dear Gromacs Users, I am trying to study ligand unbinding adopting Umbrella sampling (using Gmx 4.5.3). during my initial pull to generate configurations for umbrella windows I have pulled in the -Z direction, @ s0 legend "0 Z" @ s1 legend "1 dZ" 0.7.37361-0

[gmx-users] PMF when pulling in -Z direction

Dear Gromacs Users, I am trying to study ligand unbinding adopting Umbrella sampling (using Gmx 4.5.3). during my initial pull to generate configurations for umbrella windows I have pulled in the -Z direction, @ s0 legend "0 Z" @ s1 legend "1 dZ" 0.    7.37361    -0.33625 0.0200    7.37377

Re: [gmx-users] PMF and appending simulation: -pf and -px flags (gromacs 4.0.7)

Shay Teaching wrote: Hi everyone, Does the appending option also work when doing PMF? I have a simulation that crashed in the middle (not-gromacs-related), and now I want to continue from where it stopped. But using the -append option does not seem to continue writing to the files specified

[gmx-users] PMF and appending simulation: -pf and -px flags (gromacs 4.0.7)

Hi everyone, Does the appending option also work when doing PMF? I have a simulation that crashed in the middle (not-gromacs-related), and now I want to continue from where it stopped. But using the -append option does not seem to continue writing to the files specified in -px and -pf. Am I missi

Re: [gmx-users] PMF analysis and pull_dim (Step 6 of Justin's tutorial)

Thanks for you prompt reply! Clear and to the point. -Shay On Tue, Jun 21, 2011 at 2:03 PM, Justin A. Lemkul wrote: > > > Shay Teaching wrote: > >> Dear Gromacs Users, >> >> I've done Justin's tutorial regarding PMF/umbrella sampling and now, when >> approaching my own system I have a couple of

Re: [gmx-users] PMF analysis and pull_dim (Step 6 of Justin's tutorial)

Shay Teaching wrote: Dear Gromacs Users, I've done Justin's tutorial regarding PMF/umbrella sampling and now, when approaching my own system I have a couple of questions. (Link to the tutorial here: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.h

[gmx-users] PMF analysis and pull_dim (Step 6 of Justin's tutorial)

Dear Gromacs Users, I've done Justin's tutorial regarding PMF/umbrella sampling and now, when approaching my own system I have a couple of questions. (Link to the tutorial here: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html) My system is comprise

Re: [gmx-users] PMF curve

On Mon, May 30, 2011 at 10:10 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> >> There is not any answer? >> >> > Please have a bit of patience. I'm not your personal answer service. You > just happened to catch me at a good time this morning and I was able to

Re: [gmx-users] PMF curve

mohsen ramezanpour wrote: Dear Dr.Justin There is not any answer? Please have a bit of patience. I'm not your personal answer service. You just happened to catch me at a good time this morning and I was able to respond quickly. I have my own work to do, you know. On Mon, May 30, 20

Re: [gmx-users] PMF curve

Dear Dr.Justin There is not any answer? On Mon, May 30, 2011 at 7:58 PM, mohsen ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Yes,you are right > I need to do more sampling.But the second attached file was just to > transfer my mean :) > My final PMF curve is the first attached file. >

Re: [gmx-users] PMF curve

Yes,you are right I need to do more sampling.But the second attached file was just to transfer my mean :) My final PMF curve is the first attached file. Sorry for asking more questions.. Regarding my notes about windowses in last email and looking at FIRST attached file: Which one is my starting

Re: [gmx-users] PMF curve

mohsen ramezanpour wrote: Thank you. no,I think the problem is not zero point. Actually I maean some thing like this one.please have a look at new attached file. I just added 3 new windows in 0.3 - 0.8 But the whoe of my curve shifted upward. There is another question: Actually I pulled my

Re: [gmx-users] PMF curve

Thank you. no,I think the problem is not zero point. Actually I maean some thing like this one.please have a look at new attached file. I just added 3 new windows in 0.3 - 0.8 But the whoe of my curve shifted upward. There is another question: Actually I pulled my drug from 0.18 - 3.18 then,extra

Re: [gmx-users] PMF curve

mohsen ramezanpour wrote: Thank you for your reply Actually my system is not the same as tutorial. Then you should not equate the results, or be concerned when things look different. Every system is different. I tried to obtain protein-drug delta G. I obtained that. Yes,you are right,si

Re: [gmx-users] PMF curve

Thank you for your reply Actually my system is not the same as tutorial. I tried to obtain protein-drug delta G. I obtained that. Yes,you are right,since I don't have good computaional systems I couldn't run more than 1 ns for each windows. when there are some minimum and maximum in our curve ,Ho

Re: [gmx-users] PMF curve

mohsen ramezanpour wrote: Dear Dr.Justin Regarding to PMF curve which resulted from Umbrella sampling: I obtained the following curve. Dose it mean?Because it is not similar to yours in tutorial :( if yes,please let me know what is the Delta G value approximately? Because I don't know differen

[gmx-users] PMF curve

Dear Dr.Justin Regarding to PMF curve which resulted from Umbrella sampling: I obtained the following curve. Dose it mean?Because it is not similar to yours in tutorial :( if yes,please let me know what is the Delta G value approximately? Because I don't know difference between which points is my

Re: [gmx-users] PMF for Carbohydrate-Protein

Sai Kumar Ramadugu wrote: Dear All, I'm running set of umbrella sampling simulations to get the PMF of a disaccharide binding to a protein. I followed the tutorial provided by Justin and changed the values of necessary parameters according to my system. The mdp file for umbrella sampling sim

[gmx-users] PMF for Carbohydrate-Protein

Dear All, I'm running set of umbrella sampling simulations to get the PMF of a disaccharide binding to a protein. I followed the tutorial provided by Justin and changed the values of necessary parameters according to my system. The mdp file for umbrella sampling simulations is as follows: -

[gmx-users] PMF from pull code, unexpected results

> Michael: your mdp options indicated using US and my stance is that, > using >US, you are incorrect to say that "And you will get the SAME > result if you >do this calculation in one or in three dimensions > (pulldim NNY or pulldim >YYY)". this has nothing to do with the mdp file ... i w

[gmx-users] PMF from pull code, unexpected results

Michael: your mdp options indicated using US and my stance is that, using US, you are incorrect to say that "And you will get the SAME result if you do this calculation in one or in three dimensions (pulldim NNY or pulldim YYY)". Nevertheless, I'm a little perturbed by your call out for hel

[gmx-users] PMF from pull code, unexpected results

Looking at http://www.brunsteiner.net/tbut-pmf.gif you seem to be getting exactly what I would expect. The difference is the entropy term. Note that the spherical shell increases volume as r increases for pulldim YYY but this effect is absent for pulldim NNY. This is why you can correct as

[gmx-users] PMF from pull code, unexpected results

Dear all, I would like to calculate the potential of mean force between two molecules in aqueous solution using the pull code. For a start i performed a number of calulations with a couple of very simple model systems with settings loosely based on the example in the gmx tutorial section (see m

[gmx-users] PMF using constraints

Hi all A quick question. I want to compare a PMF curve generated using umbrella sampling with one using constraints. To use constraints do I use the exact same set up in the .mdp file but change pull = constraints. Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://list

[gmx-users] PMF on dihedral

Pomès, "Equilibrium exchange enhances the convergence rate of umbrella sampling", Chemical Physics Letters 460, 375-381 (2008) -- original message -- Message: 7 Date: Thu, 23 Sep 2010 10:26:32 +0200 From: charl...@cermav.cnrs.fr Subject: [gmx-users] PMF on dihedral To: gmx-users@gromacs

[gmx-users] PMF on dihedral

Landry, I replied earlier, but it didn't seem to make it to the list. If 2 show up then they are identical. The mailing list archive post that you cite is actually talking about a (3-point) angle and not a (4-point) dihedral angle. If you want dihedral angles, then take a look at how w

[gmx-users] PMF on dihedral

Hi I would like to perform calculations of potential of mean force on a dihedral angle. But it seems that all the options are parametrized for a PMF calculation on a distance. This question has been already posted 4 years ago (http://www.mail-archive.com/gmx-users@gromacs.org/msg00384.html) witho

[gmx-users] PMF

Hi All I have generated a potential of mean force curve for two cage molecules. The profile of the curve is very good apart from the fact that the repulsive part of the curve doesn't go above zero. My attractive tail therefore appears higher than the repulsive part. The histograms are very well be

Re: [gmx-users] PMF

abdul wadood wrote: Hi, All I am trying to calculate pmf for enzyme ligand complex using the tutorial of umbrella sampling. I have successfully created the unit cell around the protein and have solvated. The ions were also added by genion. But when I run the minimization step with the comma

[gmx-users] PMF

Hi, All I am trying to calculate pmf for enzyme ligand complex using the tutorial of umbrella sampling. I have successfully created the unit cell around the protein and have solvated. The ions were also added by genion. But when I run the minimization step with the command grompp -f minim.mdp -

[gmx-users] PMF in vacuum and pull direction

Dear Eudes: Thanks for working with me on this one! What you are getting is actually what you are asking for in your .mdp file. You restrain the Z-projection of the displacement, but do not affect the X and Y components of the displacement with pull_dim = N N Y. If you want to pull with s

[gmx-users] PMF in vacuum and pull direction (chris.ne...@utoronto.ca)

4. PMF in vacuum and pull direction (chris.ne...@utoronto.ca) > > > > Message: 4 > Date: Tue, 08 Jun 2010 12:14:34 -0400 > From: chris.ne...@utoronto.ca > Subject: [gmx-users] PMF in vacuum and pull direction > To: gmx-users@gromacs.org > Message-ID: <20100608121434.u6rhqhz400

[gmx-users] PMF in vacuum and pull direction

ate1 = 0.001 pull_k1 = 1600 Message: 4 Date: Tue, 08 Jun 2010 08:05:23 -0400 From: chris.neale at utoronto.ca Subject: [gmx-users] PMF in vacuum and pull direction To: gmx-users at gromacs.org Message-ID: <20100608080523.i6oo62he1wwc0wkg at webmail.utoronto.ca> Content-Type: text/plain

[gmx-users] PMF in vacuum and pull direction (chris.ne...@utoronto.ca)

im = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = BEN1 pull_group1 = BEN2 pull_vec1 = 0 0 1 pull_rate1 = 0.001 pull_k1 = 1600 > Message: 4 > Date: Tue, 08 Jun 2010 08:05:23 -0400 > From: chris.ne...@utoronto.ca > Subject: [gmx-users] PMF in vacuum and pull direction >

[gmx-users] PMF in vacuum and pull direction

2010 12:12:03 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] PMF in vacuum To: gmx-users@gromacs.org Message-ID: <20100527121203.orb2sq228s4ow...@webmail.utoronto.ca> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Dear

[gmx-users] PMF in vacuum and pull direction (chris.ne...@utoronto.ca)

man) > 4. vibrational spectra of glucose (Nilesh Dhumal) > > > -- > > Message: 2 > Date: Thu, 27 May 2010 12:12:03 -0400 > From: chris.ne...@utoronto.ca > Subject: [gmx-users] PMF in vacuum > To: gmx-users@gromacs.org > Message-ID: <20100

[gmx-users] PMF in vacuum

Dear Eudes: To answer your pbc vs no-pbc question, I suggest that you use pbc=no and set nstlist=0 rlist=0 rvdw=0 rcoulomb=0 so that you calculate all interactions in direct space with no cutoffs. ## Major comments that you should still investigate 1. There is no need to use a virtual atom,

[gmx-users] PMF in vacuum

Dear Eudes: Can you please elaborate on your description? What .mdp options are you using? What exactly do your curves look like (you can post pictures to photobucket or some other online service and link them here)? If you suspect that you are doing something wrong, then we need to under

[gmx-users] PMF in vacuum

Hi gmx-users, I'm trying to simulate a umbrella sampling PMF between two benzene molecules in vacuum. My protocol is working fine, my histograms have good overlap and the curves I have got are quite reasonable. However I have noticed that some options in my .mdp file can significantly change the d

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

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

Thomas Piggot wrote: Hi again, Just before I reside myself to rerunning a large number of simulations I was wondering if it is possible to just rerun the simulations where the ion is above and below the reference using pull_geometry=position. Then could I combine these with the other simulati

[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

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

Hi again, Just before I reside myself to rerunning a large number of simulations I was wondering if it is possible to just rerun the simulations where the ion is above and below the reference using pull_geometry=position. Then could I combine these with the other simulations where pull_geomet

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

Thomas Piggot wrote: Jochen thanks for your help. That was what I was afraid of you saying. Oh well, at least this will hopefully provide a useful reference so somebody doesn't make this same mistake. On a side note I noticed a couple of small issues with g_wham. Firstly the -wcorr option s

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

Jochen thanks for your help. That was what I was afraid of you saying. Oh well, at least this will hopefully provide a useful reference so somebody doesn't make this same mistake. On a side note I noticed a couple of small issues with g_wham. Firstly the -wcorr option says Input, opt. not Ou

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