Re: [gmx-users] pbc problem

On Tue, Oct 29, 2013 at 5:02 PM, shahab shariati shahab.shari...@gmail.comwrote: Dear Mark Very thanks for your reply To make this clear, center the trajectory on the water and watch the time evolution in some visualization program. I did your suggestion (center the trajectory on the

Re: [gmx-users] pbc problem

On 10/29/13 12:02 PM, shahab shariati wrote: Dear Mark Very thanks for your reply To make this clear, center the trajectory on the water and watch the time evolution in some visualization program. I did your suggestion (center the trajectory on the water). Again, drug molecule is in

Re: [gmx-users] pbc problem

On 10/27/13 8:16 AM, shahab shariati wrote: Dear Justin I want to study translocation of drug molecule in lipid bilayer. My gro file after minimization is em2.gro. After NPT-MD simulation, I obtained npt.gro and 0.xtc files. When I see trajectory by vmd, there are some things abnormal. I

Re: [gmx-users] pbc problem

Hi Shahab, What about running trjconv -pbc mol with a .tpr as input file? Cheers, Tsjerk On Sun, Oct 27, 2013 at 3:24 PM, shahab shariati shahab.shari...@gmail.comwrote: Dear Justin I attached images related to before (em2.gro) and after equilibration.

Re: [gmx-users] pbc problem

On 10/27/13 12:05 PM, shahab shariati wrote: Dear Tsjerk Wassenaar Very very thanks for your reply. I used trjconv -pbc mol. pbc problem was solved only for lipid molecules. When I see new trajectory by vmd, there are some problesm about drug molecule.

Re: [gmx-users] pbc problem

On Oct 24, 2013 8:10 AM, shahab shariati shahab.shari...@gmail.com wrote: Dear jkrieger I used 2 times trjconv tool: 1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump 2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol -center Dear Mark I selected

Re: [gmx-users] pbc problem

On 10/24/13 10:57 AM, shahab shariati wrote: Dear Mark Thank for your reply. If I show my system as 4 regions, my system before equilibration is as fallows: region (1): water + drug region (2): top leaflet of bilayer region (3): bottom leaflet of bilayer region (4): water After

Re: [gmx-users] pbc problem

As Justin said, there is no actual division between region 1 and 4. Apparently you got the free diffusion you asked for! :-) Mark On Thu, Oct 24, 2013 at 4:57 PM, shahab shariati shahab.shari...@gmail.comwrote: Dear Mark Thank for your reply. If I show my system as 4 regions, my system

Re: [gmx-users] pbc problem

I usually use -pbc nojump for my protein simulations and this works every time. Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a rectangular box. I put drug molecule in 2 position: a) drug in the center of bilayer membrane, b) drug inside water

Re: [gmx-users] pbc problem

Center on a particular lipid? Or head group? Mark On Oct 23, 2013 6:13 PM, shahab shariati shahab.shari...@gmail.com wrote: Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a rectangular box. I put drug molecule in 2 position: a) drug in the center of

Re: [gmx-users] PBC problem

Hi Yutian Yang, Yes. That is, if the chain is interacting with itself. If it remains curled up, then it won't be a problem. Cheers, Tsjerk On Thu, Jun 27, 2013 at 10:10 PM, Yutian Yang yyan...@syr.edu wrote: Hi all, I have a question about PBC. If I have a polymer chain that is longer

Re: [gmx-users] pbc problem

On 4/14/13 11:21 PM, Kieu Thu Nguyen wrote: Thank Justin ! I used the command editconf -center and i saw my membrane was in center of the box. I am stupid in that how putting the bilayer in a periodic image (instead between two periodic images as it was). Can you give me some instructions ?

Re: [gmx-users] pbc problem

Thank Justin ! I used the command editconf -center and i saw my membrane was in center of the box. I am stupid in that how putting the bilayer in a periodic image (instead between two periodic images as it was). Can you give me some instructions ? Many thanks ! On Fri, Apr 12, 2013 at 6:52 PM,

Re: [gmx-users] pbc problem

On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote: Dear All, I made a POPC bilayer and carried out embedding a protein into this membrane. But the fatal error has appeared : Fatal error: Something is wrong with your membrane. Max and min z values are 12.342000 and

Re: [gmx-users] pbc problem

hi, all My protein has 16 subunits. After I use trjconv '-pbc nojump' to remove the jump in the whole protein, there are no jump to each subunits. However, when i check pdb file of the first frame, it is shown that the subunits are not in right position. The area of interface between some

Re: [gmx-users] pbc problem

On 10/16/2007 2:31 AM, tangxuan wrote: Dear all, If pbc is full or xyz in mdp file, do i need to use the trjconv -pbc nojump to remove the jump when the protein is separate in the box after simulation and I want to calculate the rmsd of the protein? IT is not necessary to use trjconv -pbc

Re: [gmx-users] PBC problem

Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, May 16, 2007 12:49 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] PBC problem Hi Yuguang

RE: [gmx-users] PBC problem

Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, May 16, 2007 4:41 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] PBC problem Hi Yuguang, Gromacs should automatically fix the box to meet the requirements during an mdrun

RE: [gmx-users] PBC problem

://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, May 16, 2007 12:49 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] PBC problem Hi Yuguang, Warning: Triclinic box is too