On 15/05/2011 12:01 AM, Sikandar Mashayak wrote:
Hey Mark
Do you mean removing all bond definitions from topology file, when you
say well constructed topology to exclude all bonded-interactions in rerun?
I said you can decompose the bonded interactions. You can have none by
removing all bond
Dear Justin and Mark,
Thank you very much! I truly appreciate it.
Andrew DeYoung
Carnegie Mellon University
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Hey Mark
Do you mean removing all bond definitions from topology file, when you say
well constructed topology to exclude all bonded-interactions in rerun?
thanks
sikandar
On Sat, May 14, 2011 at 8:01 AM, Mark Abraham wrote:
> On 14/05/2011 10:52 PM, XAvier Periole wrote:
>
>>
>> Two things you
On 14/05/2011 10:52 PM, XAvier Periole wrote:
Two things you have to be careful about:
1- use trr trajectory files. xtc precision is not sufficient and it
will give a lot of discrepancies at least for the bonded terms.
2- set the nstlist to 1 as the neiboring list should be undated for
each fr
Two things you have to be careful about:
1- use trr trajectory files. xtc precision is not sufficient and it
will give a lot of discrepancies at least for the bonded terms.
2- set the nstlist to 1 as the neiboring list should be undated for
each frame and not every 5/10 as it is normally set
On 14/05/2011 9:11 PM, Justin A. Lemkul wrote:
Ramachandran G wrote:
Hello gmx users:
I did 1ns simulation for my system and have the trajectory and
energy files.
Now i want to see the energy of some specific residues. So, i
decompose(separated) the energy groups and edited the mdp fil
Ramachandran G wrote:
Hello gmx users:
I did 1ns simulation for my system and have the trajectory and
energy files.
Now i want to see the energy of some specific residues. So, i
decompose(separated) the energy groups and edited the mdp file.
Using the mdp file, i created a new tpr file
Hello gmx users:
I did 1ns simulation for my system and have the trajectory and energy
files.
Now i want to see the energy of some specific residues. So, i
decompose(separated) the energy groups and edited the mdp file.
Using the mdp file, i created a new tpr file and rerun the mdrun using th
Hello all
I had simulated Tip4p-2005 water system with different concentrations of MgCl2
and Cacl2 salts. I have calculated the Surface tensions of the systems and I
see that presence of the salt increases the S.T of water layer.
Now to do more analysis i want to calculate the contributions of wa
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