[gmx-users] Windows10+Visual studio 2017+CUDA8.0+Gromacs-2016.4 package

rmail/gromacs.org_gmx-developers/2016-December/009424.html) website also asked this error message but no got correct solution. Please help me to solve this problem Thanks, Yujie Liu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users

Re: [gmx-users] Windows10+Visual studio 2017+CUDA8.0+Gromacs-2016.4

Unicode format to prevent data loss3>resource-division.cpp  I don't know whether my operation is correct?? Besides, I built windows gromacs is based on this website mentioned (https://www.researchgate.net/post/I_need_to_install_GROMACS_on_windows_10_64_bit_system_Can_anyone_help_me_with_

Re: [gmx-users] Windows10+Visual studio 2017+CUDA8.0+Gromacs-2016.4

file in Unicode format to prevent data loss3>resource-division.cpp  I don't know whether my operation is correct?? Besides, I built windows gromacs is based on this website mentioned (https://www.researchgate.net/post/I_need_to_install_GROMACS_on_windows_10_64_bit_sys

[gmx-users] Some problem about the process of calculating MM-PBSA binding free energy

input parameter when I use the file of polar.mdp. The default value is 0.150. Also, I don’t add fixed concentration when I use gmx genion command by GROMACS program and only use -neutral option. Yours sincerely Yujie, liu -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] (no subject)

Thanks a lot！ In fact, I just can not confirm the value of pconc or nconc of the polar.mdp, namely under what conditions should I set “0” or “0.150”？ *Yours sincerely* *Yujie, liu* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] The small organic molecule occurred deformation during simulation

situation is normal? In addition, I employed gromos54a7.ff Yours sincerely Yujie liu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * Fo

Re: [gmx-users] The small organic molecule occurred deformation during simulation

-- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org

Re: [gmx-users] The small organic molecule occurred deformation during simulation

dihedrals. Thank you very much! Yours, Yujie liu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

Re: [gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

The .top file of protein has included itself all parameters, so now you only copy gly.gro into protein.gro and changed the number of atoms. Then using #include” ” lines to add gly.itp into protein.top in suitable position and changed [molecules] options to add the name and number of gly molecu

[gmx-users] umbrella sample Question

Hello，gromacs user I am a novice, I met some problems when I do this tutorial to learn umbrella sample, at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html. I am using gromacs 5.1.4 and the summary_distances.dat file is not complete while carrying

Re: [gmx-users] umbrella sample Question

Thanks Justin, What do you means? I have carried out gmx distance to calculate the COM distance between two groups one by one through the previous confxxx.gro by myself, however I never met some fail or warnings. Finally, it seems that I can calculate the distance from all confxxx.gro as well

Re: [gmx-users] umbrella sample Question

Thanks Justin, You are right. Your script might not be compatible with my system or software, I tried to use another python script from other people and showed a complete dat file. Thanks again Yours, Liu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.or

Re: [gmx-users] nstcomm < nstcalenergy

Hi， Firstly, you should confirm your gromacs version, gromacs 5.x certainly includes nstcalenergy options in .mdp file. So you must set nstcalenergy=1 while the default value is 10 in .mdp if you want to nstcomm=1. thanks -- Gromacs Users mailing list * Please search the archive at http://w

[gmx-users] PMF wrong when calculating dihedral angle rotate

t;https://redmine.gromacs.org/attachments/2405/gwham_error_sample.tar.gz>*) about angle by "gmx wham", I also found "profile.xvg" is wrong. I use GROMACS 2019.3. I hope some expert can give me some good advice. Whether the gromacs software can not generate correct PMF o

Re: [gmx-users] gromacs binaries for windows (Cygwin 64)

because it can use your GPU. More compile informations can been found my own wesit https://liuyujie714.com/15.html YuJie Liu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1

what happened. Best, >Christian I had reported >this bug in few days ago, please see this link: >https://redmine.gromacs.org/issues/3444 Thanks Yujie Liu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List