[gmx-users] probelm of using amber force field

Dear GMX users, I have a question about running MD simulation using amber force field. It is easy to prepare the top and gro files of protein with amber force field, but how should I prepare the itp and gro files of small molecules with GAFF force field? I know the program ANTECHAMBER and tle

[gmx-users] Re:gmx-users Digest, Vol 84, Issue 81

) > 2. Re: converging value (Mark Abraham) > 3. Re: Dangling bond error for dna (Justin A. Lemkul) > 4. probelm of using amber force field (fancy2012) > 5. Re: probelm of using amber force field (Justin A. Lemkul)

[gmx-users] Acpype error

Hi GMX users, When I ran acpype.py on my computer, I got one error like this: File "./acpype.py", line 67, in from datetime import datetime ImportError: No module named datetime I use Python-2.6.6, I do not know how this error happen, could someone help me figure it out? Thanks very much in a

[gmx-users] re: Acpype error

Dear Prof. Aldo Segura-Cabrera, Thanks very much for your reply. I just download the package of Acpype, and I ran ../acpype.py -i FFF.pdb to test acpype.py, but then I got the error. Amber11 and AmberTools 1.4 have been successfully installed on the computer. I have read the installation instruc

[gmx-users] tutorials of REMD

Dear GMX users, Are there some tutorials guiding how to do REMD simulations using gromacs? Thanks very much! All the best, qinghua -- 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

[gmx-users] question of smd

Dear GMX users, I want to do calculations of PMF based SMD and US, for the SMD calculation, first I should change the coordinates of the protein and ligand, so that the orientation of the ligand is parallel with Z axis. Could someone tell me how to deal with this step? Thanks very much! All t

[gmx-users] Re:gmx-users Digest, Vol 85, Issue 20

Dear Prof. Lemkul, Thanks very much for your reply on my problem of smd. I begin to understand how to set the vector what we like. Thanks very much for your tips. All the best, qinghua-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] constant PH simulations

Dear gmx users, Are there some tutorials on constant PH simulations using gromacs? How should I state my work? Right now I have no idea on it. -- Best wishes, Qinghua Liao Ph.D student of Tianjin University, China-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] problem of parallel run in gromacs-4.5.1

Dear GMX users, I did some MD in parallel using gromacs-4.5.1, but it failed to work! But it worked successfully when didn't use parallel version! It showed like this: Will use 12 particle-particle and 4 PME only nodes I searched the archive, and I found that someone also have this problem using

[gmx-users] problems of compiling gromacs-4.5.1

Dear GMX users, There is another question. Is there some problems of gromacs-4.5.1 when compiling it using icc, while compiling fftw-3.2.2 using gcc? Or it is just OK? Thanks very much! All the best, fancy-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

[gmx-users] the problem of gromacs-4.5.1 has been solved

Dear GMX users, Yesterday I sent the following two mails to this archive, and now my problems have been solved. Dear GMX users, I did some MD in parallel using gromacs-4.5.1, but it failed to work! But it worked successfully when didn't use parallel version! It showed like this: Will use 12 pa

[gmx-users] how to use gaff in gromacs

Dear gmx users, In gromacs-4.5.1, we can use amber force field now, but if I want to gaff, a force field of small molecules, How should I do? Could someone give me some suggestion? Thanks in advance! All the best, fancy-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/m

[gmx-users] problem of paralleled running

Dear GMX users, I have a problem when I run gromacs-4.5.1 on a cluster, I can only do paralleled running using 1 node, which is 8-cpu, but when I use more nodes, it will abort abnormally. Could someone help me figure it out? Thanks very much! All the best, fancy -- gmx-users mailing list

[gmx-users] How to prepare the two tolopogy files when doing TI calculation?

Dear GMX users, I want to do some TI calculation using GMX, and I have learned the tutorial of TI calculation from this web site http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial. So I have know how to run TI calculations. But there is still a problem. I don't know how to

[gmx-users] Re: How to prepare the two tolopogy files when doing TI calculation?

sage-ID: <4bc47b0c.4020...@anu.edu.au> > Content-Type: text/plain; charset=x-gbk; format=flowed > > On 13/04/2010 7:35 PM, fancy2012 wrote: > > Dear GMX users, > > I want to do some TI calculation using GMX, and I have learned the > > tutorial of TI calculation f

[gmx-users] about PRODRG

Dear GMX users, When I prepare the topology file of one small molecule using PRODRG, I find that the generated topology file is for another molecule. The only difference between the two molecules is that the latter one has one more double bond. How should I deal with such problems? Thanks very

[gmx-users] Thr -> Met in TI calculation

Dear GMX users, I want to calculate the relative binding free energy between a small molecule binding to a protein of Wild Type and Thr -> Met using TI, so how should I prepare the topology files of the protein using for TI calculation? Any suggestions will be highly appreciated? All the be

[gmx-users] tutorial of free energy calculations

Dear GMX users, I don't know why I can't open the tutorial of free energy calculations on this website http://www.gromacs.org/Documentation/Tutorials. Can you open it? Thanks very much! All the best, fancy-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinf

[gmx-users] epsilon_r

Dear GMX users, I find this parameter epsilon_r in a tutorial of free energy calculation, but I don't know its meaning. And also I can't find it in the manual of version 4. Could somebody explain it for me? Thanks very much! All the best, fancy-- gmx-users mailing listgmx-users@gromacs.

[gmx-users] soft-core

Dear GMX users, when I generate the input file of MD simulation using grompp, I get this error: ERROR: The soft-core power is 0 and can only be 1 or 2. I don't know how to figure it out? Could somebody give me a hand? Thanks very much in advance! Here is the mdp file: cpp = /lib

[gmx-users] Re:gmx-users Digest, Vol 74, Issue 73

message with subject or body 'help' to > gmx-users-requ...@gromacs.org > >You can reach the person managing the list at > gmx-users-ow...@gromacs.org > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of gmx-use

[gmx-users] sc_power

Hi GMX users, What is the difference between the values of sc_power, 1 and 2? Thanks very much! All the best, fancy-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Pl

[gmx-users] No default Proper Dih. types

Dear GMX users, When I run grompp, I got this error " No default Proper Dih. types", how should I figure it out? Thanks in advance! All the best, fancy-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www