Re: [gmx-users] Justin umbrella sampling tutorial......

On 5/24/12 6:35 AM, rama david wrote: Thank you Justin for these correct explanation Its really clear my lot of queries.. For the tutorial, NPT is conducted with restraints on all protein heavy atoms. The production runs are conducted by restraining only one chain for practical re

Re: [gmx-users] Justin umbrella sampling tutorial......

Thank you Justin for these correct explanation Its really clear my lot of queries.. > For the tutorial, NPT is conducted with restraints on all protein heavy > atoms. The production runs are conducted by restraining only one chain for > practical reasons. > > These is my question ; > If we are

Re: [gmx-users] Justin umbrella sampling tutorial......

On 5/24/12 8:19 AM, rama david wrote: Thank you for your reply, I am asking you again same question, EXTREMELY SORRY for my stupidity, In step six , I unable to differentiate npt and production run by mdp file as usualy we find difference by define term, I think I get meaning upto reason why

Re: [gmx-users] Justin umbrella sampling tutorial......

Thank you for your reply, I am asking you again same question, EXTREMELY SORRY for my stupidity, In step six , I unable to differentiate npt and production run by mdp file as usualy we find difference by define term, I think I get meaning upto reason why to use -DPOSRES_B, but I want to know if

Re: [gmx-users] Justin umbrella sampling tutorial......

On 5/24/12 7:40 AM, rama david wrote: Hi Justin, Thank you for your Reply Before start tutorial I read your paper, It help me a lot to understand the concept of umbrella sampling... But truly I not understand the part in six step why to use define -DPOSRES_B and not -DPOSRES, I think I m

Re: [gmx-users] Justin umbrella sampling tutorial......

Hi Justin, Thank you for your Reply Before start tutorial I read your paper, It help me a lot to understand the concept of umbrella sampling... But truly I not understand the part in six step why to use define -DPOSRES_B and not -DPOSRES, I think I miss it ... I will be a very greatfull to y

Re: [gmx-users] Justin umbrella sampling tutorial......

On 5/24/12 7:11 AM, rama david wrote: Thank you justin.. I solve script problem.. I have another query .. As mention in tutorial , In step six , we have to do brief NPT equilibration npt_umbrella.mdp link is http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/

Re: [gmx-users] Justin umbrella sampling tutorial......

Thank you justin.. I solve script problem.. I have another query .. As mention in tutorial , In step six , we have to do brief NPT equilibration npt_umbrella.mdp link is http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/npt_umbrella.mdp After these we have t

Re: [gmx-users] Justin umbrella sampling tutorial......

On 5/23/12 3:48 PM, rama david wrote: Hi Gromacs Friends, I am performing justin tutorial for umbrella sampling .. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html I encounter with following problem while using the disatances.pl

[gmx-users] Justin umbrella sampling tutorial......

Hi Gromacs Friends, I am performing justin tutorial for umbrella sampling .. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html I encounter with following problem while using the disatances.pl script 1. After command perl distances.pl I got following

Re: [gmx-users] Justin-lipid tutorials..

On 5/19/12 9:06 AM, rama david wrote: Thank you Justin.. I am sorry Because I am going to ask you the stupid questions but very imp to me ... 1. Consider your Tutorial In that Instead of using vanderwall radii adjustment to add water , I wish to use keepbyz.sh script ... In th

Re: [gmx-users] Justin-lipid tutorials..

Thank you Justin.. I am sorry Because I am going to ask you the stupid questions but very imp to me ... 1. Consider your Tutorial In that Instead of using vanderwall radii adjustment to add water , I wish to use keepbyz.sh script ... In these case What would be the value of Lower and

Re: [gmx-users] Justin-lipid tutorials..

On 5/19/12 8:23 AM, rama david wrote: Thank you Justin .. .. I goes through these link .. http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations Please Can any one clearly define me What is Lower Z and Upper Z in the|| keepbyz.sh Can keepbyz.sh use to remove the water in hydrophob

Re: [gmx-users] Justin-lipid tutorials..

Thank you Justin .. .. I goes through these link .. http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations Please Can any one clearly define me What is Lower Z and Upper Z in the keepbyz.sh Can keepbyz.sh use to remove the water in hydrophobic region without affecting the box dimensio

Re: [gmx-users] Justin-lipid tutorials..

On 5/19/12 7:49 AM, rama david wrote: Hi Gromacs friends .. I am doing justin Lipid-tutoria on lipid .. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html I completed upto the ion addition and energy minimisation.. While doing equilibrati

[gmx-users] Justin-lipid tutorials..

Hi Gromacs friends .. I am doing justin Lipid-tutoria on lipid .. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html I completed upto the ion addition and energy minimisation.. While doing equilibration I stuck with the following problem .. 1

Re: [gmx-users] justin-lipid tutorial........

On 5/8/12 8:06 AM, rama david wrote: Hi gromac friends I am performing the justin tutorials on lipids http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials I am strugling now on 3rd steps I have following queris regarding to steps ... 1. I increase the van der walls radii of

[gmx-users] justin-lipid tutorial........

Hi gromac friends I am performing the justin tutorials on lipids http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials I am strugling now on 3rd steps I have following queris regarding to steps ... 1. I increase the van der walls radii of carbon from the 0.15 to 0.375 > Is t

Re: [gmx-users] Justin-lipid tutorial..

On 5/5/12 4:01 AM, rama david wrote: Hi Gromacs Friends, I am doing the justin-lipid tutorial..Link to the tutorial is ... http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html I made the g96_53a6_lipid force field as per the instruction of tutorial.. I have some

Re: [gmx-users] Justin-lipid tutorial...

On 5/5/12 2:50 AM, rama david wrote: Hi Gromacs friends, I completed the justin lipid tutorials upto the three steps ... While performing the tutorial of lipid written by justin , I get following query.. 1. As per the tutorials we added the DPPC chain topology *; Include DPPC chain top

[gmx-users] Justin-lipid tutorial..

Hi Gromacs Friends, I am doing the justin-lipid tutorial..Link to the tutorial is ... http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html I made the g96_53a6_lipid force field as per the instruction of tutorial.. I have some queris regarding to these new force field

[gmx-users] Justin-lipid tutorial...

Hi Gromacs friends, I completed the justin lipid tutorials upto the three steps ... While performing the tutorial of lipid written by justin , I get following query.. 1. As per the tutorials we added the DPPC chain topology *; Include DPPC chain topology #include "dppc.itp" * dppc.itp file

Re: [gmx-users] Justin protein-ligand complex...

rama david wrote: On Sat, Apr 14, 2012 at 6:12 PM, Justin A. Lemkul > wrote: > > > >> Hi Justin, Thank you for reply.. >> >> >> >> My query is ..Why Pressure Coupling is off in production MD run ??? >> > > Pressure coupling is on, hence: > > pcou

Re: [gmx-users] Justin protein-ligand complex...

On Sat, Apr 14, 2012 at 6:12 PM, Justin A. Lemkul wrote: > > > >> Hi Justin, Thank you for reply.. >> >> >> >> My query is ..Why Pressure Coupling is off in production MD run ??? >> > > Pressure coupling is on, hence: > > pcoupl = Parrinello-Rahman > That means sentence ; Pressure

Re: [gmx-users] Justin protein-ligand complex...

rama david wrote: Hi Gromacs user , In justin tutorial protein-ligand complex.. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/08_MD.html the production md.mdp has following parameter for Pressure and Temperature coupling ; Temperature coupling is on t

[gmx-users] Justin protein-ligand complex...

Hi Gromacs user , In justin tutorial protein-ligand complex.. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/08_MD.html the production md.mdp has following parameter for Pressure and Temperature coupling ; Temperature coupling is on tcoupl = V-rescale

Re: [gmx-users] Justin Tutorial - Protein-Ligand

Steven Neumann wrote: Dear Gmx Users, Dear Justin, As I read in your tutorial you restrained the ligand during the quilibration: NVT and NPT. My questions is: is it required? Why cant we simply restrain the protein and let the ligand and water to move around? Will there be a huge difference

[gmx-users] Justin Tutorial - Protein-Ligand

Dear Gmx Users, Dear Justin, As I read in your tutorial you restrained the ligand during the quilibration: NVT and NPT. My questions is: is it required? Why cant we simply restrain the protein and let the ligand and water to move around? Will there be a huge difference? Thank you, Steven -- gmx

Re: [gmx-users] justin

On 07/01/11 17:00, mustafa bilsel wrote: Justin, Are you sure? I installed 4.5.3 and tried Methanol, MTH, MeOH. Nothing changed. I suggest you to try it by yourself. Don't try to remind people the help rules. JUST HELP OR DONOT HELP. We're not at your orders and shouting at people who try to

Re: [gmx-users] justin

mustafa bilsel wrote: Justin, Are you sure? I installed 4.5.3 and tried Methanol, MTH, MeOH. Nothing changed. I suggest you to try it by yourself. I did, and it works quite nicely. Don't try to remind people the help rules. JUST HELP OR DONOT HELP. I guess attempting to guide you to mo

[gmx-users] justin

Justin, Are you sure? I installed 4.5.3 and tried Methanol, MTH, MeOH. Nothing changed. I suggest you to try it by yourself. Don't try to remind people the help rules. JUST HELP OR DONOT HELP. mustafa This topology defines the [moleculetype] name as "Methanol," which is the name that needs to