Re: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1
>This sounds very much like something we should >fix. Can you file a bug report >at >https://redmine.gromacs.org/ where you can also >upload the file that you >are trying to run? Let me >know if you have any trouble with uploading the >>report - I'm eager to know 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 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_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs binaries for windows (Cygwin 64)
It is great! But, I think more effective is to enable CUDA (GPU) support. https://www.dropbox.com/s/jtk5p7bz0ppgcbf/windows_gromacs2019.3%2Bfftw%2BintelC%2B%2B%2Bcuda10.rar?dl=0 here is a CUDA version of GROMACS 2019.3 by using VS 2017 and Intel C++, which is support AVX2_256 and more effective 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PMF wrong when calculating dihedral angle rotate
Dear gmx users, I want to repeat a amber tutorial *http://ambermd.org/tutorials/advanced/tutorial17/index.htm <http://ambermd.org/tutorials/advanced/tutorial17/index.htm>* by using gromacs, which is about PMF calculation of Alanine Dipeptide Phi/Psi Rotation. Everything is ok about the process of simulation, firstly equilibrium and generate a series of configuration, then do long simulation respectively. However, When using "gmx whan -it tpr.dat -if/x pullf/x.dat -cycl" command to generate PMF curve, I found histo.xvg figure is very good but profile.xvg figure is wrong. Then I check the data of profile.xvg file, found the second column data is "-nan". I also assign -min and -max, but still wrong. Finally, I found same question on the internet, the URL is *https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-August/108093.html <https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-August/108093.html>* and *https://redmine.gromacs.org/issues/2609 <https://redmine.gromacs.org/issues/2609>* . At the same time, I repeat this a sample PMF (*https://redmine.gromacs.org/attachments/2405/gwham_error_sample.tar.gz <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 of angle? Thank you, 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Windows10+Visual studio 2017+CUDA8.0+Gromacs-2016.4
hat cannot be represented in the current code page (936). Save the 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_system_Can_anyone_help_me_with_a_step_by_step_tutorial). My GPU is GTX950m belongs to notebook, which is not support "sm_20"Thanks again,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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Windows10+Visual studio 2017+CUDA8.0+Gromacs-2016.4
nnot be represented in the current code page (936). Save the 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_system_Can_anyone_help_me_with_a_step_by_step_tutorial). My GPU is GTX950m belongs to notebook, which is not support "sm_20"Thanks again,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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Windows10+Visual studio 2017+CUDA8.0+Gromacs-2016.4 package
Hello,every one; Now, I am trying to build a windows version of gromacs with CUDA8.0. In deed, according to some information from GROMACS official website and other experience, and I have already built some version of gromacs 5.1.x and its GPU version or 2016.x with CPU. However, I meet some error messages while using CUDA to build 2016.x-gromacs by Visual studio 2017 and intel MKL and cmake packages,etc. In detail error shows following:"E:/User-software/gromacs-2016.4/src\gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_fermi.cuh(406): error : identifier "c_oneSixth" is undefined in device code 2>" and "E:/User-software/gromacs-2016.4/src\gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_fermi.cuh(406): error : identifier "c_oneTwelveth" is undefined in device code 2>". Besides, I checked this error by google,here ( https://mailman-1.sys.kth.se/pipermail/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_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_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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://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_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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.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_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 out ‘perl distances.pl’. Some values of distance between COM of Chain_A and Chain_B are empty and some distxxx.xvg files still existing. In fact, I checked out some distxxx.xvg and found which existed a value of distance but why these values can’t write into summary_distances.dat completely by commend ‘perl distances.pl’ ? There is someone met with the situation?? Thanks Yours 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] The small organic molecule occurred deformation during simulation
Mr Justin: I have tried to do energy minimization in this situation which only existing small molecule in water, I found the structure of organic molecule didn’t become distortions. I think the distortions of organic molecules are due to these stronger interactions between small molecules and enzyme, because there is a enzyme molecule in the previous simulation. Do you think this consideration is correct? In the case, do you think this phenomenon is normal? What’s more, I checked out the top file of small molecules and don’t find error and include the information of improper 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] The small organic molecule occurred deformation during simulation
Hello, users I’m a novice to study the gromacs program. Now I met some problems which the small molecule occurred deformation when energy minimization was performed. For example, the anthracene molecule became bent in the plane of C-rings, the same as phenol. I want to know whether the 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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/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_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Some problem about the process of calculating MM-PBSA binding free energy
Dear users; I met some problem when I calculated the binding free energy between protein and ligand by the g_mmpbsa program. I am sure that I had read the tutorials of its official website and some other related information, but I don’t know what should I set the value of pconc or nconc in the 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://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_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
