[gmx-users] RE:Requests

2013-10-27 Thread lloyd riggs
  >You are not allowed to post to this mailing list, and your message has >been automatically rejected. If you think that your messages are >being rejected in error, contact the mailing list owner at >gmx-developers...   Sorry I was trying to post this to the "Feature suggestion/request" site o

[gmx-users] pbc problem

2013-10-27 Thread shahab shariati
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 guess there is pbc problem. I attached these 3 f

Re: 答复: [gmx-users] error in umbralla sampling step 6

2013-10-27 Thread Justin Lemkul
Please keep the discussion on the list. On 10/27/13 5:09 AM, sunyeping wrote: Dear professor Lemkul, For warning 1: I use the npt_umbrella.mdp file you provided in step 6 in the umbralla sampling tutorial. You told us to start by running a brief NPT equilibration in each window using this mdp

Re: [gmx-users] pbc problem

2013-10-27 Thread Justin Lemkul
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 g

[gmx-users] pbc problem

2013-10-27 Thread shahab shariati
Dear Justin Please check this trajectory file (1.xtc) being smaller than 0.xtc. https://www.dropbox.com/s/9qd2l37qyfqvpox/1.xtc -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Ma

[gmx-users] mdrun cpt

2013-10-27 Thread Pavan Ghatty
Hello All, Is there a way to make mdrun put out .cpt file with the same frequency as a .xtc or .trr file. From here http://www.gromacs.org/Documentation/How-tos/Doing_Restarts I see that we can choose how often (time in mins) the .cpt file is written. But clearly if the frequency of output of .cpt

[gmx-users] pbc problem

2013-10-27 Thread shahab shariati
Dear Justin I attached images related to before (em2.gro) and after equilibration. https://www.dropbox.com/s/yjkyj5ycshvp20u/images.docx -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/

Re: [gmx-users] pbc problem

2013-10-27 Thread Tsjerk Wassenaar
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 wrote: > Dear Justin > > I attached images related to before (em2.gro) and after equilibration. > > > https://www.dropbox.com/s/yjkyj5ycshvp20u/images.docx

[gmx-users] error in umbralla sampling step 6

2013-10-27 Thread sunyeping
Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 发件人：Justin Lemkul 发送时间：2013年10月27日(星期日) 20:27 收件人：gromacs 主　题：Re: 答复: [gmx-users] error in umbralla sampling step 6 Please keep the discussion on the list. On

Re: [gmx-users] mdrun cpt

2013-10-27 Thread Justin Lemkul
On 10/27/13 9:37 AM, Pavan Ghatty wrote: Hello All, Is there a way to make mdrun put out .cpt file with the same frequency as a .xtc or .trr file. From here http://www.gromacs.org/Documentation/How-tos/Doing_Restarts I see that we can choose how often (time in mins) the .cpt file is written. B

Re: [gmx-users] error in umbralla sampling step 6

2013-10-27 Thread Justin Lemkul
On 10/27/13 11:23 AM, sunyeping wrote: Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 发件人：Justin Lemkul 发送时间：2013年10月27日(星期日) 20:27 收件人：gromacs 主　题：Re: 答复: [gmx-users] error in umbralla sampling step 6 P

[gmx-users] pbc problem

2013-10-27 Thread shahab shariati
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. https://www.dropbox.com/s/xq4s6az17buhvb8/images-2.docx If I show my system as 4 regi

Re: [gmx-users] pbc problem

2013-10-27 Thread Justin Lemkul
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. https://www.dropbox.com/s/xq4s6az17bu

Re: [gmx-users] pbc problem

2013-10-27 Thread Mark Abraham
To make this clear, center the trajectory on the water and watch the time evolution in some visualization program. Mark On Sun, Oct 27, 2013 at 5:08 PM, Justin Lemkul wrote: > > > On 10/27/13 12:05 PM, shahab shariati wrote: > >> Dear Tsjerk Wassenaar >> >> Very very thanks for your reply. >>

[gmx-users] *** Extended deadline *** CfP: 4th International Workshop on Model-driven Approaches for Simulation Engineering part of the Symposium on Theory of Modeling and Simulation (SCS SpringSim 20

2013-10-27 Thread Daniele Gianni
(Please accept our apologies if you receive multiple copies of this CFP) # CALL FOR PAPERS 4th International Workshop on Model-driven Approaches for Simulation Engineering part of the Symposium on Theory

[gmx-users] How To SOLVATE

2013-10-27 Thread Hari Pandey
Hi GROMACS users can any body tell me how do I solvate fixed number of molecules in fixed volume: for example 100 molecule water in 14*14*14 Aungstrom^3  box.  eidt conf and genbox  never can do this. One more question. Please any body help me on following warning: WARNING: masses and atomic (

Re: [gmx-users] How To SOLVATE

2013-10-27 Thread Justin Lemkul
On 10/27/13 9:30 PM, Hari Pandey wrote: Hi GROMACS users can any body tell me how do I solvate fixed number of molecules in fixed volume: for example 100 molecule water in 14*14*14 Aungstrom^3 box. eidt conf and genbox never can do this. genbox -maxsol 100 will put a block of no more t