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
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
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
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
> 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
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:
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
7 matches
Mail list logo