Re: [gmx-users] Dimer simulation problem

2011-09-26 Thread Kavyashree M
Hello, Yes i did that. but qualitatively i did not see any such clashes. But i do not know how to quantify it by calculations. Thank you with regards Kavya On Mon, Sep 26, 2011 at 5:51 PM, Sarath Chandra Dantu wrote: > > > Hello again, > > > > I centered it and then did the calculation again for

Re: [gmx-users] Dimer simulation problem

2011-09-26 Thread Sarath Chandra Dantu
> Hello again, > > I centered it and then did the calculation again for minimum image > distance > but still it showed the same graph as without centering. I tried > visualising > it > using vmd but could not see any such clashes. since I am new to vmd > I do not know whether it is possible to cal

Re: [gmx-users] Dimer simulation problem

2011-09-26 Thread Mark Abraham
On 26/09/2011 10:02 PM, Kavyashree M wrote: Hello again, I centered it and then did the calculation again for minimum image distance but still it showed the same graph as without centering. Have you followed the kind of workflow suggested here? http://www.gromacs.org/Documentation/Terminolo

Re: [gmx-users] Dimer simulation problem

2011-09-26 Thread Kavyashree M
Hello again, I centered it and then did the calculation again for minimum image distance but still it showed the same graph as without centering. I tried visualising it using vmd but could not see any such clashes. since I am new to vmd I do not know whether it is possible to calculate such clashe

Re: [gmx-users] Dimer simulation problem

2011-09-21 Thread Kavyashree M
Thanks. On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul wrote: > > > Kavyashree M wrote: > >> Dear users, >> >> I was trying to simulate a protein dimer covalently bond with >> a disulphide bond (230+230 aa long). I used usual protocol >> as used for simulation of a monomeric protein, using gr

Re: [gmx-users] Dimer simulation problem

2011-09-21 Thread Justin A. Lemkul
Kavyashree M wrote: Dear users, I was trying to simulate a protein dimer covalently bond with a disulphide bond (230+230 aa long). I used usual protocol as used for simulation of a monomeric protein, using gromacs- 4.5.3, dodecahedron box, tip4p water model and protein to box distance of 1 (-d