Re: [gmx-users] Coordinates change after minimization

try to set the value of emtol to about 1 times smaller ! On Jun 20, 2009, at 4:30 PM, Ms. Aswathy S wrote: But i am in a situation like the minimization doesn't make any change in the energy and it convergeing at 15 th step each time. So further minimization is not possible. Can you p

Re: [gmx-users] Coordinates change after minimization

Ms. Aswathy S wrote: But i am in a situation like the minimization doesn't make any change in the energy and it convergeing at 15 th step each time. So further minimization is not possible. Can you plz check the em.mdp file and tell me whetehr I have given any wrong parameter? There's nothi

Re: [gmx-users] Coordinates change after minimization

But i am in a situation like the minimization doesn't make any change in the energy and it convergeing at 15 th step each time. So further minimization is not possible. Can you plz check the em.mdp file and tell me whetehr I have given any wrong parameter? Dept. Biotechnology Ext. 3108

Re: [gmx-users] The Cut-off for coulombtype heat up the water system?

Thanks for the detailed reply. This is a really good example for the manifold of traps you can tap into when treating long range forces. Flo * Mark Abraham [2009-06-20 14:55:39 +1000]: Florian Dommert wrote: * Mark Abraham [2009-06-20 11:54:46 +1000]: When I understood the idea of the re

Re: [gmx-users] Coordinates change after minimization

On Jun 20, 2009, at 15:30, "Ms. Aswathy S" > wrote: using the g_confrm command the RMSD of the protein is 0 (Root mean square deviation after lsq fit = 4.14581e-08). It means the structure doesn't have a major change ultimately.. Please correct me if I am wrong.. You are correct. Can I

Re: [gmx-users] Coordinates change after minimization

using the g_confrm command the RMSD of the protein is 0 (Root mean square deviation after lsq fit = 4.14581e-08). It means the structure doesn't have a major change ultimately.. Please correct me if I am wrong..Can I move ahead with this minimization? Dept. Biotechnology Ext. 3108 - Origin

Re: [gmx-users] Coordinates change after minimization

Justin A. Lemkul wrote: Ms. Aswathy S wrote: Hi, After minimizing the protein -ligand complex, the co-ordinates have changed drastically.My idea about minimization was the coordinates will have minute changes only. In this case my protein is completely transferring to a new co-ordinates.Is

Re: [gmx-users] Coordinates change after minimization

Ms. Aswathy S wrote: Hi, After minimizing the protein -ligand complex, the co-ordinates have changed drastically.My idea about minimization was the coordinates will have minute changes only. In this case my protein is completely transferring to a new co-ordinates.Is that reasonable.?? The am

[gmx-users] Coordinates change after minimization

Hi, After minimizing the protein -ligand complex, the co-ordinates have changed drastically.My idea about minimization was the coordinates will have minute changes only. In this case my protein is completely transferring to a new co-ordinates.Is that reasonable.?? Thanks, Aswathy Dept. Biotech