Re: [gmx-users] Periodic Images - clarification

Dear Sir Thanks I got the point! Thanking you With Regards M. Kavyashree On Mon, Jun 27, 2011 at 12:19 PM, Tsjerk Wassenaar wrote: > Hi Kavya, > > > I did use dodecahedron cell. but how does using a dodecahedron cell > > be advantageous than any other cell when minimum image violation > > has

Re: [gmx-users] Periodic Images - clarification

Hi Kavya, > I did use dodecahedron cell.  but how does using a dodecahedron cell > be advantageous than any other cell when minimum image violation > has occurred? This is just my inquisitiveness. In a rectangular cell, such interactions may occur merely by reorientation of the solute. In that ca

Re: [gmx-users] Periodic Images - clarification

Dear Sir, I did use dodecahedron cell. On Mon, Jun 27, 2011 at 12:35 AM, Tsjerk Wassenaar wrote: > Hey, > > Maybe I missed this, but what type of unit cell did you use? You > should use a rhombic dodecahedron. > I did use dodecahedron cell. but how does using a dodecahedron cell be advantageou

Re: [gmx-users] Periodic Images - clarification

Sir, Thank you Sir for your suggestions. Probably the stability of the protein may be known only after simulation. But actually it from one of the thermophilic organisms - Thermatoga maritima. So I did not anticipate unfolding at 300K. Ur suggestions were very useful. Thanks. :) With Regards M.

Re: [gmx-users] Periodic Images - clarification

Hey, Maybe I missed this, but what type of unit cell did you use? You should use a rhombic dodecahedron. Then, I would argue that it isn't necessarily so problematic as the others put it when you have transient contacts. For the greater part of the simulation the distances in the periodic system

Re: [gmx-users] Periodic Images - clarification

Kavyashree M wrote: Sir, I would like to thank you for patiently replying for my repeatedly asked question. For most stable, well-behaved proteins, setting a suitable box size at the outset of the simulation is sufficient to avoid spurious PBC interactions. In your case, ther

Re: [gmx-users] Periodic Images - clarification

Sir, I would like to thank you for patiently replying for my repeatedly asked question. > > For most stable, well-behaved proteins, setting a suitable box size at the > outset of the simulation is sufficient to avoid spurious PBC interactions. > In your case, there are several possibilities: (1)

Re: [gmx-users] Periodic Images - clarification

Kavyashree M wrote: Dear users, I apologize for asking the same question. but I wanted a clarification regarding this I had done a simulation for 100ns which had minimum image violation after 27ns. I have asked this question several times and people have suggested me not to use the results. B

[gmx-users] Periodic Images - clarification

Dear users, I apologize for asking the same question. but I wanted a clarification regarding this I had done a simulation for 100ns which had minimum image violation after 27ns. I have asked this question several times and people have suggested me not to use the results. But I just wanted to know