Re: [gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4

Better yet, repeat something that is already out there in the literature. PMFs for water, lipids, and some amino acid side chains across the bilayer have been tested extensively. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

Re: [gmx-users] mail about contact angle

On 5/3/15 7:51 AM, vidhya sankar wrote: Dear Justin Thank you for your previous help and reply , I have Effective interaction between (LJ short range) between CNT and Water .To further enlighten this May i use contact angle and Water density profile analysis? between CNT and water Or any

Re: [gmx-users] Giving an initial velocity to a group of atoms

On 5/3/15 5:51 AM, Jashimuddin Ashraf wrote: Thanks for your reply Dr. Lemkul. I was simulating a small carbon nanotube to test the idea. So, I added three extra columns after the coordinates inside my .gro file like this- ==

Re: [gmx-users] Justin biphasic tutorial with controlled adsoption of protein

On 5/3/15 9:07 AM, James Lord wrote: Hi Justin, Thanks for the info, your assumption re long axis of the box is correct (z), here is the .gro file I have for one the oil (decane)-protein (the protein is in the middle part of the free space above the oil surface). Is that what you were talking

[gmx-users] A problem with lipids.hdb file

Hi： I am Ye Chun.I am a postgraduate in the university of science and technology of china. I’m writing a letter to you to ask for some help. I want to run a simulation with a lipid as ligand.I have some problems in order to automatically add hydrogen to lipids with charmm27 force field.

Re: [gmx-users] A problem with lipids.hdb file

On 5/3/15 9:15 PM, 叶纯 wrote: Hi： I am Ye Chun.I am a postgraduate in the university of science and technology of china. I’m writing a letter to you to ask for some help. I want to run a simulation with a lipid as ligand.I have some problems in order to automatically add hydrogen to lipids

[gmx-users] Re： Re: Problem in installation (Mahender singh and Mark Abraham )

Dear Mahender singh and Mark Abraham: Thank you for your help. Now I have installed the gromacs-4.6.1. It seems that my computer can get regressiontests-4.6.1 but cannot find regressiontests-5.1-beta. -- Best Wishes -- ***

Re: [gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4

Thanks Chris for your help I am using Isoniazid drug and the membrane model is a mixture of different lipid types (POPE,POPC,POPI,POPS,cholesterol) in a ratio mimicking the plasma membrane more closely as compared to the simple single lipid type membrane model. I have attached the PMF

Re: [gmx-users] Secondary Structure Restraints: martinize.py

Hello Tsjerk, I am executing the following command to get half helical and half random cg structure The pdb I am supplying is a helical peptide ./martinize.py -f gamma1_unmutated.pdb -x gamma1_unmutated.elnedyn.pdb -o gamma1.elnedyn.top -ss LLHHH -p backbone -ff martini22

Re: [gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4

Take a look at profiles in the literature for arginine across a bilayer. It has a maximum at the center. Probably true for any molecule with a large charge/molecular weight ratio. For more help you'd likely have to reveal your system and provide an image of the PMF. However, there is no reason

[gmx-users] mail about contact angle

Dear Justin Thank you for your  previous help and reply , I have Effective interaction between (LJ short range) between CNT and Water .To further enlighten this May i use  contact  angle and Water density profile analysis? between CNT and water Or any other post processing tool available

Re: [gmx-users] Justin biphasic tutorial with controlled adsoption of protein

Hi Justin, Thanks for the info, your assumption re long axis of the box is correct (z), here is the .gro file I have for one the oil (decane)-protein (the protein is in the middle part of the free space above the oil surface). Is that what you were talking about? I went through manual and could

Re: [gmx-users] Giving an initial velocity to a group of atoms

Thanks for your reply Dr. Lemkul. I was simulating a small carbon nanotube to test the idea. So, I added three extra columns after the coordinates inside my .gro file like this- == Georgetown Riga Oslo

Re: [gmx-users] atom freezing during simulation

On 5/3/15 1:17 AM, mah maz wrote: Dear all, I need to freeze some atoms in my system not to move during simulation. I used freezegrps and freezdim options but after simulation, I can see that the fixed atoms also moved and their coordinates changed. What can I do to fix their positions?

[gmx-users] problem of cyggmxpreprocess-6.dll

Hello, Actually, I am currently trying to install gromacs 4.5.2 on windows 8 with Cygwin + Cmake platform.I installed Cmake 3.1.3, FFTW 3.3.4 and gromacs 4.5.2 using procedure mentioned in installation guide.my laptop is core i3 processes and I am using single precision method. But even after