[gmx-users] g_sham experimental weighting with temperature

Dear, Please could you suggest me some reference or description about the mentioned "experimental energy and temperature weighting" of g_sham tool? Can I safely use this energy and Temperature weighting procedure to obtain reliable PMF plots from a T-REMD simulation? In case of using g_sham

[gmx-users] g_sham experimental weighting with temperature

Hi, I hope someone can suggest me any reference or description about the mentioned "experimental energy and temperature weighting" of the tool g_sham. Can I safely use this weighting procedure to obtain reliable PMF plots from a T-REMD simulation? In case of using g_sham with the weighting

[gmx-users] g_sham experimental weighting with temperature

Dear users, I hope someone can suggest me any reference or description about the mentioned "experimental energy and temperature weighting" of the tool g_sham. Can I safely use this weighting procedure to obtain reliable PMF plots from a T-REMD simulation? In case of using g_sham with the

Re: [gmx-users] g_sham

, August 22, 2015 4:16 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_sham Dear Micholas, The awk command that you have suggested as: awk -v x=coord1min -v y=coord2min 'BEGIN{while(getline yourfile_first_coordinate_here.xvg){if($0!~/#/$0!~/@/$0!~//){a[$1]=$2}}{if($0

Re: [gmx-users] g_sham

nabajyoti.gosw...@gmail.com Sent: Saturday, August 22, 2015 4:16 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_sham Dear Micholas, The awk command that you have suggested as: awk -v x=coord1min -v y=coord2min 'BEGIN{while(getline yourfile_first_coordinate_here.xvg){if($0

Re: [gmx-users] g_sham

list for GROMACS users Subject: Re: [gmx-users] g_sham Thanks for the reply Micholas. I read the special discussion on dPCA at your provided link. But that is a fact of small peptide penta-alanine. I actually completed a 100 ns simulation of a outermembrane protein (of 239 amino acid

Re: [gmx-users] g_sham

...@maillist.sys.kth.se on behalf of Naba nabajyoti.gosw...@gmail.com Sent: Friday, August 07, 2015 12:57 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] g_sham Dear All, I searched a lot more things about g_sham in the mailing list and eventually getting confused

Re: [gmx-users] g_sham

-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Naba nabajyoti.gosw...@gmail.com Sent: Thursday, August 13, 2015 4:17 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_sham Thanks for the reply Micholas. I read the special discussion

Re: [gmx-users] g_sham

for GROMACS users Subject: Re: [gmx-users] g_sham Thanks for the reply Micholas. I read the special discussion on dPCA at your provided link. But that is a fact of small peptide penta-alanine. I actually completed a 100 ns simulation of a outermembrane protein (of 239 amino acid residues) with 284

Re: [gmx-users] g_sham

To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] g_sham Dear All, I searched a lot more things about g_sham in the mailing list and eventually getting confused with the inputs. Just make me clear about: 1. Is it feasible to obtain free energy landscape (FEL) from a 2D projection (using

[gmx-users] g_sham

Dear All, I searched a lot more things about g_sham in the mailing list and eventually getting confused with the inputs. Just make me clear about: 1. Is it feasible to obtain free energy landscape (FEL) from a 2D projection (using g_anaeig) of index groups (say some loop's atoms) which are used

[gmx-users] g_sham segmentation fault

Dear Users, I am trying to make a free energy plot using g_sham utility of gromacs. I have 10 data points. I am getting the energ.xvg file when I run the utility with my reaction coordinates. However, when I include the weights, it shows segmentation fault. I tried reducing the points to 10,