[gmx-users] How to obtain a approperiate PDB file of DNA?
Hi, all... I have a question on the pdb files of DNA: How can I obtain an appropriate DNA pdb file for GMX simulation? I just download some pdb files from Internet, but it is not compatible for GMX, saying that the residue was not found in rtp file. How can I solve this problem? Are the references available on this problem? Furthermore, if I want to get several DNA pdb files with increasing degree of polymerization (such as 10, 20, 50 etc.). How can I achieve this goal? Thanks a lot! Ming ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to obtain a approperiate PDB file of DNA?
Hi, Mark: I want to check the chain length of DNA on the translocation time through a nanopore. So the DNA chains with different polymerization but the same monomer structure is necessary. How can I solve this problem? Does anybody has a optimized DNA pdb file for GMX simulation? Thanks a lot!! Ming 2009/4/10 Mark Abraham mark.abra...@anu.edu.au li ming wrote: Hi, all... I have a question on the pdb files of DNA: How can I obtain an appropriate DNA pdb file for GMX simulation? I just download some pdb files from Internet, but it is not compatible for GMX, saying that the residue was not found in rtp file. How can I solve this problem? Are the references available on this problem? Perhaps you should start by searching for some tutorial material with emphasis on these types of simulation. Furthermore, if I want to get several DNA pdb files with increasing degree of polymerization (such as 10, 20, 50 etc.). How can I achieve this goal? This may or may not be easy to achieve, but you should start by describing it more fully. What are you wanting to polymerize, and what do you mean by that word? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ming Li Institute of Chemistry,Chinese Academy of Sciences Zhongguancun, Beijing, 100080, P. R. China Tel: +86-10-13811601014 / 62564829 E-mail: lim...@iccas.ac.cn / mingli1...@gmail.com ... Knowledge is a city to the building of which every human being brought a stone. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] incorporate multi proteins into a cell?
Hi! All... I want to explain my problem in detail. I just want to do the GPU test of gromacs simulation. And I just scheme to build cells with consequently increasing number of proteins--such as 1, 2, 5, 10 et.al--to examine the GPU efficiency on gromacs simulation. So I want to know how to incorporate multi protein into a cell? Because the periodic boundary condition is not supported in OpenMM software of GPU simulation, So I wanna further information on how to remove the PBC in the cell? Any involved comment is appreciated! Ming ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to merge the protein and lipid bilayer in a cell?
Hi! All.. I wanna do the simulation on the translocation of protein in the lipid bilayer, but how can I insert protein into lipid bilayer, and keep the protein on the on the top of the center of lipid bilayer? Maybe I need some detailed steps to achieve this goal, for I am a novice of gromacs software... Any involved comment is appreciated. Thanks a lot!!! Ming ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] three questions about GMX modeling...
Hi, All: I have three questions: (1) How can I add more than one protein into a cell with PBC, maybe 10 proteins? How can I modify the command of editconf and genbox to achieve the above function? (2) How to remove the PBC of the cell? I use the option '-pbc no' in the editconf fiat, but it can not be recognized by GMX? (3) If I want to add some nanostructure into the lipid bilayer structure, how can I modify the position of the added molecules in the cell? Thanks a lot!!! Ming ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GPU calculation of GROMACS in Windows System
Hi! all: I am informed in OPENMM website that the OPENMM can accelerate GPU calculation of GROMACS in Windows System. How can I apply this method to my study? Any ideas will be welcomed!!! My display card in my PC is in ATI series, and the lib of OPENMM is not provided in OPENMM website...So I guess I can do this simulation only in Windows. I just know that OPENMM zephyr could achieve this goal, but only AMBER forcefield is permitted. Did GROMACS have the WINDOWS version after GROMACS 4? Or can I use cygwin to do simulation in WIndows using GPU. Thanks a lot!! Ming Li ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx in GPU calculation
Dear all: I am troubled with this problem: when I run mdrun_openmm fias in GPU calculation of gmx, I met the following information: Back Off! I just backed up md.log to md.log.2 Getting Loaded... Reading file 1.tpr, VERSION 4.0.3 (single precision) Note: tpx file_version 58, software version 59 Segmentation fault What does it mean? How can I run the this simulation? Thanks a lot... Ming 2009/3/13 li ming mingli1...@gmail.com Dear all: I am troubled with this problem: when I run mdrun_openm faaia in GPU calculation of gmx, I met the following information: *Back Off! I just backed up md.log to md.log.2* ** *Getting Loaded...* ** *Reading file 1.tpr, VERSION 4.0.3 (single precision)* ** *Note: tpx file_version 58, software version 59* ** *Segmentation fault* What does it mean? How can I run the this simulation? Thanks a lot... Ming -- Ming Li Institute of Chemistry,Chinese Academy of Sciences Zhongguancun, Beijing, 100080, P. R. China Tel: +86-10-13811601014 / 62564829 E-mail: lim...@iccas.ac.cn / mingli1...@gmail.com ... Knowledge is a city to the building of which every human being brought a stone. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gmx in GPU calculation
Dear all: I am troubled with this problem: when I run mdrun_openm faaia in GPU calculation of gmx, I met the following information: *Back Off! I just backed up md.log to md.log.2* ** *Getting Loaded...* ** *Reading file 1.tpr, VERSION 4.0.3 (single precision)* ** *Note: tpx file_version 58, software version 59* ** *Segmentation fault* What does it mean? How can I run the this simulation? Thanks a lot... Ming ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] About 8 core CPUs platform
Hi!!! I have a question about computing platform. My primary idea is as follows... Could I install two Intel Core 2 Duo CPUs (each with 4 cores , such as Core 2 Q9500) in one main board, just like a PC? It is appropriate for computer simulation? What about its computing stability? We choose VMD to visualize the result of the molecular dynamics simulation. What display card can be used well in Fedora 8 Linux? Is there any additional advice to me for disposing computing platform? Thanks a lot!!! Ming Li Dec.29th,08 -- Ming Li Institute of Chemistry,Chinese Academy of Sciences Zhongguancun, Beijing, 100080, P. R. China Tel: +86-10-13811601014 / 62564829 E-mail: lim...@iccas.ac.cn / mingli1...@gmail.com ... Knowledge is a city to the building of which every human being brought a stone. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
