Re: [gmx-users] Had anybody modied the source code of gromacs

2010-04-18 Thread Mark Abraham
On 19/04/2010 3:58 PM, 聂雪川 wrote: > Hello gmx-users, > I just have one question about modifing the source code of > gromacs4.0.7.For I want to control the motion of one certain atom (e.g. > atom 200).I added some codes like /"if(n==my_atom)xprime[n][d] = > x[n][d]+...;"/ in the functionstatic /v

Re: [gmx-users] CG-MD simulation of protein, always crash with protein

2010-04-18 Thread Trang
On Fri, Apr 16, 2010 at 5:17 PM, Martti Louhivuori wrote: > On 15 Apr 2010, at 18:06, Trang wrote: > >> My target system is a protein with lipid molecules added randomly (using >> GENBOX). Running MD, I expect to >> > > I hope you're using a larger van der Waals distance (0.24nm or so) when > inse

Re: [gmx-users] output of dssp

2010-04-18 Thread Justin A. Lemkul
Hsin-Lin wrote: Hi, I used do_dssp_d to analyze my data. The commend was written in this way: do_dssp_d -f a.gro -s a.tpr -n a.ndx -sc dssp.xvg There are three output, #ddXB2RJu.1#, ss.xpm and dssp.xvg, be generated. What is the first output file? A backup file of one of the intermediates

[gmx-users] output of dssp

2010-04-18 Thread Hsin-Lin
Hi, I used do_dssp_d to analyze my data. The commend was written in this way: do_dssp_d -f a.gro -s a.tpr -n a.ndx -sc dssp.xvg There are three output, #ddXB2RJu.1#, ss.xpm and dssp.xvg, be generated. What is the first output file? It is generated automatically but with nothing inside. And in m

RE: [gmx-users] manual eq. 4.74-4.75 (dihedral restraints) head scratcher

2010-04-18 Thread Berk Hess
> Date: Sat, 17 Apr 2010 14:58:22 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] manual eq. 4.74-4.75 (dihedral restraints) head > scratcher > > > > Daniel L. Ensign wrote: > > Hello gmx-users, you rock and rollers, > > > > Equations 4.74 and 4.75

Re: [gmx-users] Re: slow speed

2010-04-18 Thread Carsten Kutzner
On Apr 16, 2010, at 1:40 AM, Shuangxing Dai wrote: > I am not running in parallel. Right now I just changed links order from 12 to > 4. It is still slow. While I change to shift, not Ewald, it finished 1 > steps in 10 mins. In the paper: > J Comput Chem. 2005 Dec;26(16):1701-18. > GROMACS:

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

2010-04-18 Thread Jochen Hub
rasoul nasiri wrote: Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? If you want to place several identical solutes with genbox -ci, then you could copy the file vdwradii.dat to