[gmx-users] Is Total Test time for regression tests relevant to real performance?

Hi All, Today I compiled GROMACS 5.1.2 on two machines. One has i7-3770k, the other one has i7-4770k. The odd thing I saw was it took 264.77 sec to complete the regression tests on the 4770k machine while it took 150.05 sec on the 3770k machine. The specs of the 3770k machine are lower in all

Re: [gmx-users] Correct method to do Cartesian PCA

Hi Tsjerk, I replicated their settings in their papers. The system size I used is larger than what they had. Could you elaborate on the reference used for fitting? Thank you so much. Cheers, Bin Message: 3 Date: Fri, 8 Jan 2016 18:29:26 +0100 From: Tsjerk Wassenaar To:

Re: [gmx-users] Correct method to do Cartesian PCA

rset=UTF-8 Hi Bin, The procedure is correct, provided you ensured that the input trajectory did not have PBC jumps. But the paper you refer to is on dihedral angle PCA... Cheers, Tsjerk On Jan 7, 2016 23:06, "Bin Liu" <fdusuperstr...@gmail.com> wrote: > Hi All, > >

[gmx-users] Correct method to do Cartesian PCA

Hi All, I am trying to reproduce the Cartesian PCA results for ALA3 in water by Altis et al. (Fig.2 of Dihedral angle principal component analysis of molecular dynamics simulations. http://dx.doi.org/10.1063/1.2746330 ) It is probably the most well-known PCA analysis results. I created a system

Re: [gmx-users] g_select syntax

Dear Teemu, Thank you for your explanation. Now I understand why the first selection gives more residues as it's simply a superset of the second selection. I just realized to accomplish what I initially want, i.e., to obtain the residue index list of LIPID whose center of mass is within 1.0 nm of

[gmx-users] g_select syntax

Hi Everyone, I am recently puzzled by the syntax and behaviour of g_select. I want to obtain the residue index list of LIPID whose center of mass is within 1.0 nm of the surface of protein. In my case, each LIPID molecule consists of only one residue. I wrote the selection.dat as follows, and set

Re: [gmx-users] Any way to use GROMACS 4.6.x and 5 together

-5.0_bin ~/gromacs_bin If you're in a unix shell, you need to re-open it for .bashrc to take effect. I assumed you're running GROMACS under some Linux/Unix platform but probably the same can be achieved on any other OS. Hope this helps, t On 2 Aug 2014 00:32, Bin Liu fdusuperstr

[gmx-users] How deuterium order parameters computed?

Hi Everyone, I have a question about the implementation details of g_order. When I was reading literatures, I found several interpretations of how the deuterium order parameters are computed. One is calculate S_{ij} first, then S_{CD} = \frac{2}{3} S_{xx} + \frac{1}{3} S_{yy}. Another approach