[gmx-users] Re: distance_restraints

Hi, Tsjerk, Oh, so that's it . Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009146.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Re: distance_restraints

Hi Maggin, The constraints are typically used during MD simulation to allow larger time steps. Cheers, Tsjerk On Fri, Jun 14, 2013 at 9:39 AM, maggin wrote: > Hi, Tsjerk, > > I have one question that in what situation people do constraint ? > > Thank you very much! > > maggin > > > > -- > Vi

[gmx-users] Re: distance_restraints

Hi, Tsjerk, I have one question that in what situation people do constraint ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009144.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- g

[gmx-users] Re: distance_restraints

Hi, Tsjerk I want equlibration enough time, so set NVT time 10ns , but simulation collapse at 7ns, protein have 7 fragments. Before NVT, I just do one time of steep energy minimization. So, I want first use constraint do steep, cg in vacuum, then add water, do steep, cg with constraint, then

Re: [gmx-users] Re: distance_restraints

Hi Maggin, Why do you run EM with constraints? Cheers, Tsjerk On Thu, Jun 13, 2013 at 10:53 AM, maggin wrote: > Hi, Justin, > > It's seems no problem at steep energy minimization, except lose H atoms > connect with C, the superposition are very well. > > When I use Pymol to align the NMR st

[gmx-users] Re: distance_restraints

Hi, Justin, It's seems no problem at steep energy minimization, except lose H atoms connect with C, the superposition are very well. When I use Pymol to align the NMR structure and the structure after cg minimization, because cg is after steep, so same as steep, they lose H atoms that connect wi

[gmx-users] Re: distance_restraints

Hi, Justin, I use Pymol to align the NMR structure and the structure after steep minimization, find problematic areas are superposition very well, while all the problematic areas have same character, that after steep minimization, Amino acid will lose some H atoms connect with C

Re: [gmx-users] Re: distance_restraints

On 6/12/13 12:10 AM, maggin wrote: Hi, Justin, You are right, I should first fix the bad geometry. I check 1dx0.pdb, and the problematic areas are: atom1 atom2 1 N1+ (GLY124 N) 4 H (GLY124 HT3) 181 C (PRO137 CD)182 H

[gmx-users] Re: distance_restraints

Hi, Justin, You are right, I should first fix the bad geometry. I check 1dx0.pdb, and the problematic areas are: atom1 atom2 1 N1+ (GLY124 N) 4 H (GLY124 HT3) 181 C (PRO137 CD)182 H (PRO137 HD1) 262 H (PHE14