Re: [gmx-users] gromacs 2.1

Hi, you can get it from git. "git log {file}" shows the history and git show {version}:{file} gives you a specific version. In this case you can use: git show 74b20ce9:src/tools/g_order.c Roland On Sat, Jun 11, 2011 at 10:11 PM, wrote: > Dear users: > > Does anybody have the source code for gr

[gmx-users] g_energy

Hello all, I have a quick question about extracting energy values from g_energy. I used an old trajectory to extend my simulation from 1 ns to 5 ns. Energy values from extended run do not take into account values of the first 1 ns. Is there any way to combine energies of these two runs? or I shoul

Re: [gmx-users] g_energy

Juliette N. wrote: Hello all, I have a quick question about extracting energy values from g_energy. I used an old trajectory to extend my simulation from 1 ns to 5 ns. Energy values from extended run do not take into account values of the first 1 ns. Is there any way to combine energies of

[gmx-users] Regarding H-bond autocorrelation

Hello, I am calculating the H-bond autocorrelation using g_hbond for my system, but after plotting I have observed that the value for c(t) is reaching to negative, as far as I know it can not be negative as the probability can not be negative...please suggest where is the problem.. -- --

[gmx-users] nonormalize option in g_rotacf

Hi, I am having some seeming difficulty with the -normalize option in g_rotacf, which calculates rotational autocorrelation functions of molecules. My system consists of 254 SPC/E water molecules. I equilibrated (3 ns, md integrator) and ran production dynamics (2 ns, md integrator) in the NV

Re: [gmx-users] nonormalize option in g_rotacf

Andrew DeYoung wrote: Hi, I am having some seeming difficulty with the -normalize option in g_rotacf, which calculates rotational autocorrelation functions of molecules. My system consists of 254 SPC/E water molecules. I equilibrated (3 ns, md integrator) and ran production dynamics (2 n

[gmx-users] Dissociation of Ligand-reg

Dear Sir, Greeting! I convey my thanks to your kind reply for rising whatever doubts and troubles in gromacs. I able to do my simulation with desire ligand following your instruction. Now I am interested to simulate the dissociation of bound ligand particularly one molecule among three. Sir, I n

[gmx-users] reg PME usage

Dear justin,   Thank you for your previous reply.   When i study the effect of ionic strength on stability Which Parameter of Electrostatics Should  i use? . If I use usual PME  Then will it interfere it with  result?. Because My system has Non zero charge  I went