[gmx-users] pulling along hexane-water interface

Sorry forgot to write the subject in previous mail. Dear gmx-users, We intend to perform free energy calculations by pulling a polypeptide along water-hexane interface. We need to pull the polypypeptide from the water layer towards the hexane layer (crossing the interface). For this we position

[gmx-users] Pulling

Dear users, I have a sytem including protein, lipids, and water. My protein is in center of the box. Now i want it stays at one side of the box. Which tool or command should i use to pull the protein to a any mong muốn location ? Thankful for any help ! Thu -- gmx-users mailing list

[gmx-users] pulling simulations

Dear Sir, In pulling simulations how to set pull_rate and pull_k .On which basis we can set these values. -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

Re: [gmx-users] pulling simulations

The force should not probably exceed kT product too much... Dr. Vitaly Chaban On Wed, May 29, 2013 at 3:19 PM, Sathish Kumar sathishk...@gmail.comwrote: Dear Sir, In pulling simulations how to set pull_rate and pull_k .On which basis we can set these values. --

Re: [gmx-users] pulling simulations

On 5/29/13 9:19 AM, Sathish Kumar wrote: Dear Sir, In pulling simulations how to set pull_rate and pull_k .On which basis we can set these values. There is no systematic way to set these values, at least none that I know of. Everyone has their own impression of

[gmx-users] pulling simulations

Sir, I want to do pulling simulations for membrane protein and gold nanoparticles. Can you please suggest me some tutorials. Thank You -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users *

[gmx-users] Pulling along dihedral angle as the reaction coordinate

Dear gromacs users, I want to calculate PMF using pull code in gromacs, taking a psi angle as the reaction coordinate. I have a doubt where it is possible with the geometry options, currently available in gromacs? Thanks and regards Neeru -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Pulling along dihedral angle as the reaction coordinate

On 4/15/13 2:27 AM, neeru sharma wrote: Dear gromacs users, I want to calculate PMF using pull code in gromacs, taking a psi angle as the reaction coordinate. I have a doubt where it is possible with the geometry options, currently available in gromacs? This is an application of either

[gmx-users] Pulling along dihedral angle as the reaction coordinate

I came across one such application name PLUMED plugin for gromacs, for dihedral restraints as the reaction coordinate. If you can suggest any other application for the same, kindly let me know. --Thanks Neeru On 4/15/13 2:27 AM, neeru sharma wrote: Dear gromacs users, I want to

[gmx-users] pulling direction in Umbrella sampling

Dear Users, I am using umbrella sampling method for unwinding of a peptide from binding site. I have to pull peptide in -X (negative direction). Can anyone suggest me keyword for this purpose. Should I use pulling_dim = Y N N or have to define some other keywords. I will be thankful for every

Re: [gmx-users] pulling direction in Umbrella sampling

On 4/14/13 2:09 AM, Kshatresh Dutta Dubey wrote: Dear Users, I am using umbrella sampling method for unwinding of a peptide from binding site. I have to pull peptide in -X (negative direction). Can anyone suggest me keyword for this purpose. Should I use pulling_dim = Y N N or have to

[gmx-users] Pulling and g_wham - Two analysis problems

Dear Gromacs users, I encountered two problems in using g_wham to calculate pmf curves from a pulling simulation. My system consists of a water molecule which is pulled through a bilayer (the reference group). I used gromacs 4.5.6 with the following pull code options: pull=

Re: [gmx-users] Pulling and g_wham - Two analysis problems

On 2/8/13 6:00 AM, Steinbrecher, Thomas (IBG) wrote: Dear Gromacs users, I encountered two problems in using g_wham to calculate pmf curves from a pulling simulation. My system consists of a water molecule which is pulled through a bilayer (the reference group). I used gromacs 4.5.6 with

Re: [gmx-users] Pulling ion - US

On 12/10/12 9:01 AM, Steven Neumann wrote: Dear Gmx Users, I am pulling away cation from the protein glutamic acid residue with: pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance

Re: [gmx-users] Pulling ion - US

On Mon, Dec 10, 2012 at 2:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/10/12 9:01 AM, Steven Neumann wrote: Dear Gmx Users, I am pulling away cation from the protein glutamic acid residue with: pull= umbrella pull_geometry = distance ; simple distance increase

Re: [gmx-users] Pulling ion - US

Would you also specify in each US window specific residue instead of the whole protein? Sreven On Mon, Dec 10, 2012 at 2:47 PM, Steven Neumann s.neuman...@gmail.com wrote: On Mon, Dec 10, 2012 at 2:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/10/12 9:01 AM, Steven Neumann wrote: Dear

Re: [gmx-users] Pulling ion - US

On 12/10/12 10:50 AM, Steven Neumann wrote: Would you also specify in each US window specific residue instead of the whole protein? That really depends on whether the residue-ion distance reflects the desired reaction coordinate and if doing so is superior to using the protein-ion

[gmx-users] Pulling ligand - Different Profiles (Force vs time)

As a side note: The rupture process is a stochastic process, so a single rupture force is meaningless, since it is a distributed property. So you need to do many simulations to get the distribution / average rupture force. It that same like equilibrium properties, one doesn't determine them

[gmx-users] Pulling ligand - Different Profiles (Force vs time)

Dear Gmx Users, I obtained a protein-ligand complex from 100ns simulation. Now I am pulling my ligand away from the protein after the energy minimzation in water and equilibration of 100ps (two coupling baths: Protein, LIG_Water_and_ions). Then I proceed my pulling : grompp -f pull.mdp -c

Re: [gmx-users] Pulling ligand - Different Profiles (Force vs time)

On 6/27/12 7:48 AM, Steven Neumann wrote: Dear Gmx Users, I obtained a protein-ligand complex from 100ns simulation. Now I am pulling my ligand away from the protein after the energy minimzation in water and equilibration of 100ps (two coupling baths: Protein, LIG_Water_and_ions). Then I

Re: [gmx-users] Pulling ligand - Different Profiles (Force vs time)

On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/27/12 7:48 AM, Steven Neumann wrote: Dear Gmx Users, I obtained a protein-ligand complex from 100ns simulation. Now I am pulling my ligand away from the protein after the energy minimzation in water and

Re: [gmx-users] Pulling ligand - Different Profiles (Force vs time)

On 6/27/12 9:36 AM, Steven Neumann wrote: On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/27/12 7:48 AM, Steven Neumann wrote: Dear Gmx Users, I obtained a protein-ligand complex from 100ns simulation. Now I am pulling my ligand away from the protein after

Re: [gmx-users] Pulling ligand - Different Profiles (Force vs time)

Thank you Justin. On Wed, Jun 27, 2012 at 2:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/27/12 9:36 AM, Steven Neumann wrote: On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/27/12 7:48 AM, Steven Neumann wrote: Dear Gmx Users, I obtained a

[gmx-users] Pulling - ligand outside the box

Dear Gmx Users, I pulled my ligand away from the protein and I found out that after getting rid of PBC (trjconv -pbc whole) my ligand goes outside the box? Is it fine or should I increase my box as I want to run umbrella sampling? Thanks, Steven -- gmx-users mailing list

Re: [gmx-users] Pulling - ligand outside the box

On 8/06/2012 8:35 PM, Steven Neumann wrote: Dear Gmx Users, I pulled my ligand away from the protein and I found out that after getting rid of PBC (trjconv -pbc whole) There is no magic way to get rid of PBC, and -pbc whole is certainly not it. Read trjconv -h and see

[gmx-users] Pulling multiple groups

Hi I am trying to use the pull code of gromacs (version 4.5.5) to constrain the com of a number of groups (labelled CIT, CIT1, CIT2...) to a reference group (labelled GOLD). This is the segment of the .mdp file I have used: ;CoM pull calculations pull= constraint

Re: [gmx-users] Pulling multiple groups

Wright, Louise wrote: Hi I am trying to use the pull code of gromacs (version 4.5.5) to constrain the com of a number of groups (labelled CIT, CIT1, CIT2...) to a reference group (labelled GOLD). This is the segment of the .mdp file I have used: ;CoM pull calculations pull

Re: [gmx-users] Pulling multiple groups

Hi Justin, thanks for your reply. Yes the distances get a lot larger and are definitely not just fluctuating. It is hard to demonstrate this without showing you the whole file which is huge. However, I have used the same input files with gromacs 4.5.4 just now and it works- I think it might

Re: [gmx-users] Pulling multiple groups

Wright, Louise wrote: Hi Justin, thanks for your reply. Yes the distances get a lot larger and are definitely not just fluctuating. It is hard to demonstrate this without showing you the whole file which is huge. However, I have used the same input files with gromacs 4.5.4 just now and

[gmx-users] pulling force vs free energy

Hi, What is the relation between pulling force and free energy of binding. can we relate the maximum pulling force with the free energy. for example, 2 systems has the maximum pulling force and free energy as below from umbrella sampling and g_wham analysis, max. force

Re: [gmx-users] pulling force vs free energy

Vijayaraj wrote: Hi, What is the relation between pulling force and free energy of binding. can we relate the maximum pulling force with the free energy. for example, 2 systems has the maximum pulling force and free energy as below from umbrella sampling and g_wham analysis,

[gmx-users] pulling force vs free energy

Message: 4 Date: Wed, 16 Nov 2011 09:34:02 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] pulling force vs free energy To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ec3c9da.7040...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format

Re: [gmx-users] pulling force vs free energy

Vijayaraj wrote: Message: 4 Date: Wed, 16 Nov 2011 09:34:02 -0500 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] pulling force vs free energy To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users

Re: [gmx-users] pulling force vs free energy

A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] pulling force vs free energy To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org** Message-ID: 4ec3c9da.7040...@vt.edu mailto:4EC3C9DA.7040400@vt.**edu4ec3c9da.7040...@vt.edu

[gmx-users] pulling code

Dear Adam: I have a number of questions listed below. But first, I think it would be useful if you explain exactly what you want to accomplish and how you tried to do this with non-modified code and what problem you ran into that caused you to modify the code. After you outline that,

[gmx-users] pulling code

Hi all, I am trying to measure the energy curve of unwinding the SNARE protein complex. This requires pulling the C-termini of two helices apart from each other, while fixing certain other parts of the complex. To do this I excluded the reference group, so that all groups were pulled to absolute

[gmx-users] Pulling a ligand out of protein cavity

Dear gromacs users, I am trying to pull a ligand out of a cavity of a membrane protein (along the Z axis). Problem is, that with every pull settings I have tried the ligand gets stuck on the protein's center of mass. How can I make it go all the was to the bulk water? It always gets stuck on the

Re: [gmx-users] Pulling a ligand out of protein cavity

Shay Teaching wrote: Dear gromacs users, I am trying to pull a ligand out of a cavity of a membrane protein (along the Z axis). Problem is, that with every pull settings I have tried the ligand gets stuck on the protein's center of mass. How can I make it go all the was to the bulk water?

Re: [gmx-users] Pulling a ligand out of protein cavity

Thanks for you prompt reply - I'll try that and post back. -SA On Tue, May 31, 2011 at 4:46 PM, Justin A. Lemkul jalem...@vt.edu wrote: Shay Teaching wrote: Dear gromacs users, I am trying to pull a ligand out of a cavity of a membrane protein (along the Z axis). Problem is, that with

[gmx-users] pulling of a metal

Dear all, I am trying to pull a metal out of the protein binding pocket following a cavity in the protein structure. I followed the tutorial, but I find few problems: 1) When the metal leaves the binding pocket, some ligands follow the metal, even that I restrained the position of protein atoms

Re: [gmx-users] pulling of a metal

Jon Mujika wrote: Dear all, I am trying to pull a metal out of the protein binding pocket following a cavity in the protein structure. I followed the tutorial, but I find few problems: 1) When the metal leaves the binding pocket, some ligands follow the metal, even that I restrained the

Re: [gmx-users] Pulling

Thank you again for your reply On Wed, Mar 16, 2011 at 7:35 PM, chris.ne...@utoronto.ca wrote: 2-When you limit your sampling phase space,it can make some Errors, Because you may ignore some important regions(where you don't know them and you can't predict there). I agree with the idea

Re: [gmx-users] Pulling

Dear Chris Thanks for your reply 2-When you limit your sampling phase space,it can make some Errors,Because you may ignore some important regions(where you don't know them and you can't predict there). In the other hands,When we pull drug along a line,although we had not restrain it, but in fact

[gmx-users] Pulling

2-When you limit your sampling phase space,it can make some Errors, Because you may ignore some important regions(where you don't know them and you can't predict there). I agree with the idea that underlies your point, but it is not a problem. You don't need to sample all intervening phase

[gmx-users] Pulling

Dear All Afew question about Pulling in Umberella Sampling 1-the goal of pulling is making some primary structures (in different distances) to do umberella sampling for each one of them. I can make these states by transporting my ligands along a vector to prepare these primary structures.Is this

[gmx-users] Pulling

1. yes. it is acceptable. It is different, but neither method is de facto better. 2. to enhance convergence by limiting the amount of phase space that must be sampled. Changing the restraints can change the profile, but if you care only about the integrated standard binding free energy

[gmx-users] pulling

Dear All I am using this configuration.mdp file for pulling.this is the same as umbrella sampling,of course I have changed some parts of it according to my problem(protein-ligand free energy).but when i use grompp this warning is occuring. WARNING 1 [file configuration.mdp, line unknown]:

Re: [gmx-users] pulling

mohsen ramezanpour wrote: Dear All I am using this configuration.mdp file for pulling.this is the same as umbrella sampling,of course I have changed some parts of it according to my problem(protein-ligand free energy).but when i use grompp this warning is occuring. The only reason I can

[gmx-users] pulling

Dear All I want to pull my ligand from protein which is docked to it for generating configurations for umbrella sampling. But my ligand is located in a hole inside of protein. If I pull it along the line which is connecting COMs of them,the ligand may be arrested(constraint)inside of hole. Am I

[gmx-users] Pulling Simulation Query

Hi ... Just wondering if there's a way, during pulling simulations, to immobilise say the C-terminus of the protein. I've been running through the 'Umbrella Sampling' tutorial with my own protein. Within this tutorial the ChainB is used as the immobile reference - so it is this that is

[gmx-users] pulling experiment

Dear gmx-users I want to design such kind of computer experiment: For a system composed of non-bonded three layers (carbon nanotubes, graphene, or whatever), I want to fix layer0 (the group name) to exactly (0,0,0), and pull layer2 by a constant force, for example, along positive x all the time.

Re: [gmx-users] pulling experiment

Sorry for my mistake about the group names. I was confused just to find it difficult to simultaneously fix one group (layer0) but pull another (layer2). It is possible to fix an absolute reference and pull layer2, but layer0 might follow the motion of layer2. For such experiment, the relative

Re: [gmx-users] pulling experiment

Xiaohua Zhang wrote: Dear gmx-users I want to design such kind of computer experiment: For a system composed of non-bonded three layers (carbon nanotubes, graphene, or whatever), I want to fix layer0 (the group name) to exactly (0,0,0), and pull layer2 by a constant force, for example,

Re: [gmx-users] pulling experiment

Xiaohua Zhang wrote: Sorry for my mistake about the group names. I was confused just to find it difficult to simultaneously fix one group (layer0) but pull another (layer2). It is possible to fix an absolute reference and pull layer2, but layer0 might follow the motion of layer2. For such

[gmx-users] pulling of ligand

Dear GMX user I am working on enzyme ligand complex and want to calculate pmf of the complex. I have successfully energy minimized and equilibrated the system. But when I pull the ligand from the complex using the md_pull.mdp file then instead of ligand the protein is come out of the system. I

Re: [gmx-users] pulling of ligand

abdul wadood wrote: Dear GMX user I am working on enzyme ligand complex and want to calculate pmf of the complex. I have successfully energy minimized and equilibrated the system. But when I pull the ligand from the complex using the md_pull.mdp file then instead of ligand the protein is

[gmx-users] pulling simulation with implicit solvent

Hi all, Can anyone please give me a mdp file for running pulling simulations in implicit solvent using GROMACS? Thanks in advance Samrat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] Pulling water

Sorry, I want to ask the same question I had a week ago. I need your advice in COM PULL. This is a part of article which describes methodology ...with respect to the atomic distance between the carbonyl carbon of the substrate and the oxygen atom of the identified nucleophilic water, a

[gmx-users] PULLING

Sorry for so disordered questions... 3. use the pull code. I don't know exactly what you want to do here...perhaps harmonically restrain the distance between the two mentioned groups to some specified value? No need to rename the water, just make an index group. The problem is that I don't know

[gmx-users] PULLING

Sorry for so disordered questions... 3. use the pull code. I don't know exactly what you want to do here...perhaps harmonically restrain the distance between the two mentioned groups to some specified value? No need to rename the water, just make an index group. The problem is that I don't know

Re: [gmx-users] PULLING

Алексей Раевский wrote: Sorry for so disordered questions... 3. use the pull code. I don't know exactly what you want to do here...perhaps harmonically restrain the distance between the two mentioned groups to some specified value? No need to rename the water, just make an index group.

[gmx-users] PULLING

Sorry for so disordered questions... 3. use the pull code. I don't know exactly what you want to do here...perhaps harmonically restrain the distance between the two mentioned groups to some specified value? No need to rename the water, just make an index group. The problem is that I don't know

[gmx-users] PULLING

Hi all. I have to reproduce an experiment from the article Identification of the nucleophilic factors and the productive complex for the editing reaction by leucyl-tRNA synthetase (by Yohsuke Hagiwara a,b, Osamu Nureki c, Masaru Tateno a,b,*). This is one of the steps of education I have to

[gmx-users] PULLING

First let me mention that I only scanned the mammoth manuscript snippet. Nevertheless, I'll try to address your questions. 1. You are physically able to use spc in place of tip3p. Whether or not that is a good idea is up to you to decide. Read the literature including the spc, tip3p, and

[gmx-users] pulling

Hey, has anyone actually succeeded doing pulling with gromacs 4.0.5 keeping the distance between a froozen and a non froozen group (so not pulling into a direction but just applying the harmonic potential to the distance). If so, could you send me the mdp file showing how you set up the whole

[gmx-users] Pulling in GROMACS 4.0.3

Hi again, I am trying to pull apart a CG protein (to verify CG results with those of already published works using atomistic MD). Using the previous suggestions, my new pull code is the following: title= Martini cpp = /usr/bin/cpp integrator

Re: [gmx-users] Pulling in GROMACS 4.0.3

Johnny Lam wrote: Hi again, I am trying to pull apart a CG protein (to verify CG results with those of already published works using atomistic MD). Using the previous suggestions, my new pull code is the following: By pull apart, do you mean to unwind the secondary structure of the

Re: [gmx-users] Pulling in GROMACS 4.0.3

Hi Justin, Thx for the reply. By pull apart, I just wanted to expose an 'activation site' by using a force. It is somewhat similar to pulling two domains of a protein away from each other. I'm not aiming to undo any secondary structure. I hope this is clearer. Thanks again! --Johnny Johnny

Re: [gmx-users] Pulling in GROMACS 4.0.3

Hi again, I actually figured it out. Turns out, it was a stupid formatting error in the .mdp file. Even though I had it as shown, it didn't read the pull command because it wasn't formatted properly (thought it was still a part of the first line). Sorry guys. --Johnny Hi Justin, Thx for the

[gmx-users] pulling

Hey, I appear to have serious trouble understanding how to set up the pulling properly. I have many configurations of a protein partially adsorbed to a froozen surface (the configs differ in the amount of the protein that has been desorbed). Now I want the pulling to keep the distance of the

RE: [gmx-users] pulling

answers if you do not have pbc issues. Berk Date: Fri, 31 Jul 2009 12:13:07 +0200 From: alexander.h...@mytum.de To: gmx-users@gromacs.org Subject: [gmx-users] pulling Hey, I appear to have serious trouble understanding how to set up the pulling properly. I have many configurations

RE: [gmx-users] pulling

in. With distance you could be unlucky that it takes the distance in the opposite direction. Berk Date: Fri, 31 Jul 2009 12:32:13 +0200 From: alexander.h...@mytum.de To: gmx-users@gromacs.org Subject: Re: [gmx-users] pulling Thx for the quick reply! I use 4.0.5, pbc z=yes Box height = 17.5nm gld

Re: [gmx-users] Pulling a CG protein

Hi Johnny, I am not familiar with pulling and even less with gromacs but I would be very cautious in using the MARTINI force field for the kind of simulation you are doing. This CG model has not been tested at all for this and it might not be very good at it! But I would be very interested

Re: [gmx-users] Pulling a CG protein

Hi Xavier (and Johnny), I quite agree with what Xavier says. Still I would like to point out that we have used CG models to pull on them and at least qualitatively they behave quite reasonably, although these models have never been parameterized or systematically tested with this kind of

Re: [gmx-users] Pulling a CG protein

Marc Baaden wrote: Hi Xavier (and Johnny), I quite agree with what Xavier says. Still I would like to point out that we have used CG models to pull on them and at least qualitatively they behave quite reasonably, although these models have never been parameterized or systematically tested with

Re: [gmx-users] Pulling a CG protein

On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote: Marc Baaden wrote: Hi Xavier (and Johnny), I quite agree with what Xavier says. Still I would like to point out that we have used CG models to pull on them and at least qualitatively they behave quite reasonably, although these

Re: [gmx-users] Pulling a CG protein

XAvier Periole wrote: On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote: Marc Baaden wrote: Hi Xavier (and Johnny), I quite agree with what Xavier says. Still I would like to point out that we have used CG models to pull on them and at least qualitatively they behave quite reasonably,

Re: [gmx-users] Pulling a CG protein

On Jul 30, 2009, at 12:10 PM, David van der Spoel wrote: XAvier Periole wrote: On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote: Marc Baaden wrote: Hi Xavier (and Johnny), I quite agree with what Xavier says. Still I would like to point out that we have used CG models to pull on

Re: [gmx-users] Pulling a CG protein

Hi, Just picking up the following bits of the conversation: David van der Spoel wrote: What does this boil down to? If you want to apply MD tools to get an accurate force curve *now*, use all atom models. [..] x.peri...@rug.nl said: This is of course the idea, but then comes the problem of

Re: [gmx-users] Pulling a CG protein

Hi XAvier, Marc, and David, Thank you so much for the reply and encouragement ;-). Please forgive me as I am trying to learn how to reply to the thread that I started. With regards to the fun discussion, it was my original intent to compare the results of pulling with the MARTINI forcefield (if

[gmx-users] Pulling a CG protein

Dear gromacs users, Hi, I am trying to pull apart a relatively large protein (CG using the martini force field) by pulling on two groups in opposite directions. To do this, I will be using the following .mdp file. However, I am almost certain that it contains errors: title=

Re: [gmx-users] pulling molecule insert into DPPC lipid bilayer

wara boon wrote: Dear, gmx-users I can't pull molecule into DPPC lipid bilayer. I want file.mdp to use MD simulations. Please. That won't fix your problems. If you need to learn, do some tutorials and read some documentation and try things out. Mark

[gmx-users] pulling of molecule in GROMACS 4.03

Dear Sir, I want to pull a molecule called PRO from the lipid membrane DPP. To do this I have written the .mdp file as following from the help of gromacs mannual 4.0 . But when I try to make .tpr file from the .gro file, it says that segmentation fault. Can you please

[gmx-users] Pulling in 4.0 - Any documentation?

Dear All, Where can I find documentation about the pull code in Gromacs 4.0? As far as I understand old style of setting up pulling simulations in separate file does not work any more, but I can't figure out how to transfer pulling params correctly to mdp file. Any help is appreciated! P.S.

RE: [gmx-users] Pulling in 4.0 - Any documentation?

Hi, Currently there is a beta 4.0 manual on ftp.gromacs.org. The mdp options can also be found in: share/html/online/mdp_opt.html Berk Date: Wed, 19 Nov 2008 03:33:47 -0800 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] Pulling in 4.0 - Any documentation? Dear

Re: [gmx-users] Pulling in 4.0 - Any documentation?

Semen Esilevsky wrote: Dear All, Where can I find documentation about the pull code in Gromacs 4.0? As far as I understand old style of setting up pulling simulations in separate file does not work any more, but I can't figure out how to transfer pulling params correctly to mdp file. Any help

Re: [gmx-users] Pulling in 4.0 - Any documentation?

-users@gromacs.org Sent: Wednesday, November 19, 2008 1:57:19 PM Subject: Re: [gmx-users] Pulling in 4.0 - Any documentation? Semen Esilevsky wrote: Dear All, Where can I find documentation about the pull code in Gromacs 4.0? As far as I understand old style of setting up pulling simulations

[gmx-users] pulling with dodecahedral box

Hallo! I have got a question on the afm pulling option. I am trying to pull a single atom into the direction of the center of mass of a protein in my simulation cell. Everything works fine with a cubic box. When I use a truncated dodecahedral box, at time step 1 the atom is suddenly located at

Re: [gmx-users] pulling with dodecahedral box

Hi Mareike, Probably your simulation starts off with remapping your pull-atom over the periodic boundaries. Make sure that the atom and the protein are properly placed inside the rhombic dodecahedron (actually the brick representation of it) before the simulation. Note that Gromacs performs

[gmx-users] pulling force

Dear Users, I would like to use a force that during the dynamics will bring closer my two molecules. Is there any way to implement this function? Thanks in advance, Giacomo Bastianelli ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] pulling force

Giacomo Bastianelli wrote: Dear Users, I would like to use a force that during the dynamics will bring closer my two molecules. Is there any way to implement this function? Section 6.2 of the manual. Mark ___ gmx-users mailing list

[gmx-users] pulling code problem.

My pull.ppa file is as follows. verbose = noruntype = afmgroup_1 = Fe group_2 = His93reference_group = 4Nweights_1 = 55.847 reference_weights = 14.0067 14.0067 14.0067 14.0067weights_2 = 14.0067 1.008 12.011 12.011 12.011 14.0067 1.008 12.011 12.011 14.0067 12.011 15.9994reftype = comreflag =