Re: [gmx-users] problem with undistribution of water

That problem is called periodic boundaries. Try inserting a second bilayer to get, at least on one axis, a water layer between the two lipid layers, if you want to prevent PBC for a part of the waters. Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical

Re: [gmx-users] query for g_sas

On Fri, 7 Mar 2008 00:42:46 +0530 (IST) Dilraj Lama [EMAIL PROTECTED] wrote: Hello gmx users, I suppose this is one of the more common subject post going around in the mailing list. I have gone through the list and have gathered some information on the subject. But I have some

RE: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling

Date: Thu, 6 Mar 2008 13:57:31 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling Berk Hess a écrit : Hi, I now realized that my fix what completely incorrect. I wanted to multiply the margin of

RE: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling

From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: RE: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling Date: Fri, 7 Mar 2008 10:14:00 +0100 Date: Thu, 6 Mar 2008 13:57:31 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users]

RE: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions

Dave, -pbc mol did not work, however -pbc atom did. Also noted here: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ Thank you. -Rob Date: Fri, 7 Mar 2008 07:42:41 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re:

Re: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions

rob yang wrote: Dave, -pbc mol did not work, however -pbc atom did. Also noted here: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ Thank you. did not work is not good enough a description. However, the functionality has changed, intentionally. The -pbc atom breaks molecules

RE: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions

Dave, I am using it for visualization for now. -pbc mol gave me the same output as -pbc whole, which was a cubic box with broken protein. -pbc atom gave the dodecahedron box and intact protein. But since the functionality of -pbc mol has changed, and may not be applicable to visualization

[gmx-users] .gro files generation for a certain time-step interval in a simulation

Hi All, I wonder if anyone knows what is the command to use in order to generate .gro files for a certain time-step interval in a simulation? For example, if I have a completed simulation of 10 ns long and I want to output (somehow) 10 .gro files each at 1st ns, 2nd ns, 3rd ns and so on out from

Re: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions

rob yang wrote: Dave, I am using it for visualization for now. -pbc mol gave me the same output as -pbc whole, which was a cubic box with broken protein. -pbc atom gave the dodecahedron box and intact protein. But since the functionality of -pbc mol has changed, and may not be applicable to

RE: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions

Okay, my mistake. Here's what each option gave me (all with -ur compact): -pbc whole: broken protein, rectangular box -pbc mol: intact protein, rectangular box, part of protein sticking outside the box -pbc atom: intact protein, dodecahedron box but -pbc mol -ur compact should give you a

Re: [gmx-users] .gro files generation for a certain time-step interval in a simulation

trjconv -dump time Huey Ling Tan wrote: Hi All, I wonder if anyone knows what is the command to use in order to generate .gro files for a certain time-step interval in a simulation? For example, if I have a completed simulation of 10 ns long and I want to output (somehow) 10 .gro files each

[gmx-users] Position restraints on a lipid bilayer

Hello, I am looking to add position restraints to some atoms of a lipid bilayer. There seem to be a lot in the list archives on this subject, but I am still a tad confused. What I would like to do is to position restrain the phosphorus atoms in only one leaflet of the bilayer. So how do I

[gmx-users] Skewed box using Parrinello-Rahman pressure coupling

Hi Berk, I´ll try the setting you proposed and let you know wether it worked. Stephane, thanks for your tip but I already use h-bonds as the constraints option. Best Luther Berk Hess a écrit : Hi, I now realized that my fix what completely incorrect. I wanted to multiply the margin of

[gmx-users] ED analysis, domain rotation, DynDom

Hi I have a done number of MD simulations of a two domain protein with different ligands and also in the apo state. Comparing these simulations I see varying degrees of domain rotation of the one domain relative to the other which I want to quantitatively measure and I was thinking of using

Re: [gmx-users] Position restraints on a lipid bilayer

toma0052 wrote: Hello, I am looking to add position restraints to some atoms of a lipid bilayer. There seem to be a lot in the list archives on this subject, but I am still a tad confused. What I would like to do is to position restrain the phosphorus atoms in only one leaflet of the

[gmx-users] Noive to gromacs : MD for zeolitic system

Dear Gromacs users, I would like to try Gromacs to conduct MD on my system which has, Zeolite( Ti,Si,O elements with pore and extraframework cations like Na+), water as solvent and some counterions in water. I am intrested to study the ionexcahnge in this system. I tried Dl_POLY but because of

Re: [gmx-users] Noive to gromacs : MD for zeolitic system

anjaiah Nalaparaju wrote: Dear Gromacs users, I would like to try Gromacs to conduct MD on my system which has, Zeolite( Ti,Si,O elements with pore and extraframework cations like Na+), water as solvent and some counterions in water. I am intrested to study the ionexcahnge in this system. I

[gmx-users] Error of moleculetype

Dear gromacs users, Hi, I have encounter the following error,after addition of Sodium ions to my system as it has -5.0 charge and before minimization. Fatal error: No such moleculetype Na I have checked errors of gromacs but I didn't understand that.Is I will write the word NA below the

Re: [gmx-users] Error of moleculetype

s lal badshah wrote: Dear gromacs users, Hi, I have encounter the following error,after addition of Sodium ions to my system as it has -5.0 charge and before minimization. Fatal error: No such moleculetype Na I have checked errors of gromacs but I didn't understand that.Is I will write