Right :)
On Wed, Oct 27, 2010 at 2:27 PM, leila karami wrote:
> Dear Tsjerk
>
> Thus, as you said, Xtc file obtained from trjconv –pbc nojump only concerns
> visualization. Thus, can I use old xtc file (with out –pbc nojump) for
> analysis such as interfacial waters and water mediated hydrogen bo
Hi Leila,
2.xtc should contain all that you want.
My point was that you shouldn't need to separate protein/dna and
solvent into two trajectories to be combined later.
Note that this only concerns visualization. You can do distance and
H-bond calculations on the original trajectory, as the relevant
Hi Leila,
Maybe you're better off trying:
1. trjconv -pbc nojump # choose system for output
2. trjconv -center -pbc mol # choose protein/dna for centering, system
for output
Centering is done before removing PBC, so you should be safe with two passes.
You might also want to play with -ur t
On Oct 27, 2010, at 10:05 AM, leila karami wrote:
> Hi Carsten
>
> Thanks for your answer. You got my case very well.
>
> I understand your mean as follows:
>
> 1) Trjconv –f a.xtc –s a.tpr –o b.xtc –pbc mol (output group=water)
>
> 2) Trjconv –f a.xtc –s a.tpr –o c.xtc –pbc noju
Hi,
with the nojump option, your water molecules will slowly
diffuse out of the "home" box and appear far away from your
protein if you display the MD system with VMD or pymol.
You can split your trajectory in two parts (using index groups)
and use different options on them individually:
a) on th
On 2010-10-27 09.40, David van der Spoel wrote:
I did simulation of protein-dna complex in water solvent. After
simulation, two strands of dna was separated when I displayed my a.xtc
with VMD.I used (trjconv –f a.xtc –s a.tpr –n a.ndx –o b.xtc –pbc
nojump) and problem fixed. But now I have ano
6 matches
Mail list logo
