Re: [gmx-users] Minimum periodic distance

2011-05-30 Thread Kavyashree M
Hello Sir, Thanks for your reply sir. I will check to it. With regards M. Kavyashree On Mon, May 30, 2011 at 4:59 PM, Tsjerk Wassenaar wrote: > Hi Kavya, > > There is no way to correct for such things afterwards. But I would > guess it's not much of a problem in your case. If a situation wit

Re: [gmx-users] Minimum periodic distance

2011-05-30 Thread Tsjerk Wassenaar
Hi Kavya, There is no way to correct for such things afterwards. But I would guess it's not much of a problem in your case. If a situation with a short distance is only transient, it is unlikely to affect the simulation. On the other hand, you may have secondary, indirect effects due to water orde

Re: [gmx-users] Minimum periodic distance

2011-05-30 Thread Kavyashree M
Hello Sir, The difference between the rcolumb (1.4nm) and minimum image distance that was obtained between two hydrogen HZ2 and HZ3 atoms of 2 lysine residues (1.39714nm) is 0.00286nm = 0.0286Ang, Since this distance is smaller than bond distance between hydrogen and nitrogen which is ~1.0Ang, So

Re: [gmx-users] Minimum periodic distance

2011-05-29 Thread Mark Abraham
On 05/30/2011 03:36 PM, Kavyashree M wrote: Hello Sir, I saw the 21824th frame, it dint look unusually stretched when I superposed against the initial pdb file. there atoms were hydrogen atoms of two lysine residues.. And in the entire strttch of 100ns simulation this is the only periodic image

Re: [gmx-users] Minimum periodic distance

2011-05-29 Thread Kavyashree M
Hello Sir, I saw the 21824th frame, it dint look unusually stretched when I superposed against the initial pdb file. there atoms were hydrogen atoms of two lysine residues.. And in the entire strttch of 100ns simulation this is the only periodic image interaction observed, Is it possible to corre

Re: [gmx-users] Minimum periodic distance

2011-05-29 Thread Kavyashree M
Hello sir, I had used a dodecahedron cell for simulation. I have run the simulation for 100ns, did you man I have to restart the simulation again? Thanking you Kavya On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar wrote: > Hi Kavya, > > > "shortest periodic distance is 1.39714 (nm) at time 2

Re: [gmx-users] Minimum periodic distance

2011-05-29 Thread Tsjerk Wassenaar
Hi Kavya, > "shortest periodic distance is 1.39714 (nm) at time 21824 (ps), > between atoms 2062 and 3688" > where 2062 is a protein atom and 21824 is a water molecule. 21824 is the time in ps at which the two atoms indicated, 2062 and 3688, are at the short distance given. You can dump the frame

Re: [gmx-users] Minimum periodic distance

2011-05-28 Thread Mark Abraham
On 28/05/2011 2:16 PM, Kavyashree M wrote: Dear users, I ran a simulation of a protein in water with rlist = rcoloumb = 1.4nm, rvdw = 1.0nm, with PME and the distance between in the periodic was set to a minimum of 2.0 i.,e distance between protein and cell edge was set to 1.0nm, Even then, when

[gmx-users] Minimum periodic distance

2011-05-27 Thread Kavyashree M
Dear users, I ran a simulation of a protein in water with rlist = rcoloumb = 1.4nm, rvdw = 1.0nm, with PME and the distance between in the periodic was set to a minimum of 2.0 i.,e distance between protein and cell edge was set to 1.0nm, Even then, when I ran g_mindist, there was a message stating