[gmx-users] PBC problem in bilayer system

Dear Tsjerk Thanks for your reply. I think that there is another problem, except for visualization. I obtained the Z coordinate (along the bilayer normal) of the center of mass of the 4 drug molecules (violet, blue, red and green lines) and DPPC lipid bilayer (black line) as a function of

Re: [gmx-users] PBC problem in bilayer system

On 9/15/14 4:52 AM, shahab shariati wrote: Dear Tsjerk Thanks for your reply. I think that there is another problem, except for visualization. I obtained the Z coordinate (along the bilayer normal) of the center of mass of the 4 drug molecules (violet, blue, red and green lines) and DPPC

[gmx-users] PBC problem in bilayer system

Dear Justin Very very thanks for your time and consideration. Excuse me for many questions. I want to make sure my trajectory is valid and accurate for analysis and then for writing related paper. My last question is that can I use this trajectory for doing analysis such as g_traj, g_dist,

Re: [gmx-users] PBC problem in bilayer system

On 9/15/14 12:11 PM, shahab shariati wrote: Dear Justin Very very thanks for your time and consideration. Excuse me for many questions. I want to make sure my trajectory is valid and accurate for analysis and then for writing related paper. It is. My last question is that can I use

[gmx-users] PBC problem in bilayer system

Dear Justin Thanks for your answer. You said The raw output of g_traj in this case is not very useful I want to know position and location of drug molecules relative to the DPPC bilayer during simulation time. In your opinion, how should I use this tool (g_traj)? Is g_dist appropriate for

Re: [gmx-users] PBC problem in bilayer system

On 9/15/14 3:12 PM, shahab shariati wrote: Dear Justin Thanks for your answer. You said The raw output of g_traj in this case is not very useful I want to know position and location of drug molecules relative to the DPPC bilayer during simulation time. In your opinion, how should I use

Re: [gmx-users] PBC problem in bilayer system

On 9/13/14 7:59 AM, shahab shariati wrote: Dear Justin you said The -trans option takes a vector where you specify the amount of translation to apply I do not know what vector should be considered in -trans option. Well, what have you tried? You need to shift your system along z, the

[gmx-users] PBC problem in bilayer system

Dear Justin Thanks for your reply. I inserted 4 drug molecules in close vicinity to the membrane surface in water phase, in one side of bilayer (for example, top). In the different frames of trajectory, some of drug molecules (one or two drug molecules) are seen in other side of bilayer

Re: [gmx-users] PBC problem in bilayer system

On 9/14/14 8:43 AM, shahab shariati wrote: Dear Justin Thanks for your reply. I inserted 4 drug molecules in close vicinity to the membrane surface in water phase, in one side of bilayer (for example, top). In the different frames of trajectory, some of drug molecules (one or two drug

[gmx-users] PBC problem in bilayer system

Dear Justin I did MD simulation on the NPT ensemble: pcoupl = Berendsen pcoupltype = semiisotropic ref_p = 1.0 In this condition, to solve this problem, what should I do? -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] PBC problem in bilayer system

On 9/14/14 8:58 AM, shahab shariati wrote: Dear Justin I did MD simulation on the NPT ensemble: pcoupl = Berendsen pcoupltype = semiisotropic ref_p = 1.0 In this condition, to solve this problem, what should I do? I have already

[gmx-users] PBC problem in bilayer system

Dear Justin I did following: trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -trans 6.46063 6.57889 9 Based on your reply*, *I translated all system along the z. I used x and y according to box dimension. I used 9, instead of z dimension (8.30034), for z. When I see **.xtc using vmd, problem

Re: [gmx-users] PBC problem in bilayer system

On 9/14/14 9:52 AM, shahab shariati wrote: Dear Justin I did following: trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -trans 6.46063 6.57889 9 Based on your reply*, *I translated all system along the z. I used x and y according to box dimension. I used 9, instead of z dimension

Re: [gmx-users] PBC problem in bilayer system

On 9/14/14 10:29 AM, shahab shariati wrote: Dear Justin Based on your previous reply, I used following: trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -pbc mol –trans 0 0 7 When I see **.xtc using vmd, unfortunately, problem was not solved. Please see the following link:

Re: [gmx-users] PBC problem in bilayer system

Hi, Just a small side note. There's nothing intrinsically nonsensical about translating more than a box size. The PBC are translation invariant, so you can do anything and have the system be fine. However, for visualization, translating one box length, and put the stuff back in the box, makes as

[gmx-users] PBC problem in bilayer system

Dear Justin you said The -trans option takes a vector where you specify the amount of translation to apply I do not know what vector should be considered in -trans option. please guide me to solve this problem as soon as possible. Best, -- Gromacs Users mailing list * Please search the

[gmx-users] PBC problem in bilayer system

Dear Gromacs users Unfortunately, no one did not answer my previous question about selection of appropriate option for trjconv -pbc to solve pbc problem. For preparation of initial system, I inserted 4 drug molecules in close vicinity to the membrane surface in water phase, in one side of

Re: [gmx-users] PBC problem in bilayer system

On 9/11/14 8:01 AM, shahab shariati wrote: Dear gromacs users When I see trajectory file using vmd, there is state showed in following link: https://www.dropbox.com/s/g8i934atodrb7te/figure2.TIF?dl=0 in initial structure, all 4 drugs were inserted in water phase, in one side of bilayer.

[gmx-users] PBC problem in bilayer system

Dear Justin Very thanks for your answer. Unfortunately, I am beginner in MD simulation of bilayer membrane systems. Based on your answer (You can try the translation options of trjconv in conjunction with -pbc mol), should I use following command? trjconv –trans –pbc mol trjconv –pbc nojump

[gmx-users] PBC problem in bilayer system

Dear Michael Carter Thanks for your answer. I used -pbc nojump Followed by -fit rot+trans Unfortunately, my problem was not solved. Please guide me to solve this problem. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] PBC problem in bilayer system

Dear gromacs users I did MD simulation of my system containing DPPC lipids + water molecule and 4 drug molecules. I saw trajectory file using VMD. Unfortunately, drug molecules jump across the box. How to resolve this PBC problem? which of -pbc options (none, mol, res, atom, nojump, cluster

Re: [gmx-users] PBC problem in bilayer system

Hi, Try -pbc nojump Best, Mike On 09/09/2014 15:11, shahab shariati shahab.shari...@gmail.com wrote: Dear gromacs users I did MD simulation of my system containing DPPC lipids + water molecule and 4 drug molecules. I saw trajectory file using VMD. Unfortunately, drug molecules jump across

Re: [gmx-users] PBC problem in bilayer system

Also if you want to fix the position on the centre of mass (no rotating or translating) try -pbc nojump Followed by -fit rot+trans Remember to use you new .xtc from your no jump command for the -fit command. Then view in vmd and your molecules will not jump, rotate, or translate around the box.