[gmx-users] 回复: 回复: 回复: Problem with Potential Mean Force calculation

- 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Justin Lemkul 发送时间: 2020年4月23日星期四 下午6:17 收件人: gmx-us...@gromacs.org 主题: Re: [gmx-users] 回复: 回复: Problem with Potential Mean Force calculation On 4/22/20 10:40 AM, Rolly Ng wrote: > Dear Justin and Vu, > > I think I have solve

[gmx-users] 回复: 回复: Problem with Potential Mean Force calculation

tell us your reaction coordinate is range from about 2-7nm but WHAM fit from 0-10nm is so strange Best regards, On Tue, Apr 21, 2020 at 4:49 PM Justin Lemkul wrote: > > > On 4/21/20 10:40 AM, Rolly Ng wrote: > > Dear Justin, > > > > I cut the x-axis to 8nm but I ha

[gmx-users] 回复: 回复: Problem with Potential Mean Force calculation

, Apr 21, 2020 at 4:49 PM Justin Lemkul wrote: > > > On 4/21/20 10:40 AM, Rolly Ng wrote: > > Dear Justin, > > > > I cut the x-axis to 8nm but I have uploaded the original histogram > > plot > to > > RG. Please have a look again, thank you. > > It'

[gmx-users] 回复: Problem with Potential Mean Force calculation

? Thanks, Rolly -邮件原件- 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Justin Lemkul 发送时间: 2020年4月21日星期二 下午7:09 收件人: Discussion list for GROMACS users 主题: Re: [gmx-users] Problem with Potential Mean Force calculation On 4/21/20 2:08 AM, Rolly Ng wrote: > > Dear Gromac

[gmx-users] Problem with Potential Mean Force calculation

has gone wrong? Thanks very much, Rolly Ng -- 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

[gmx-users] Protonated ligand free energy calculation in water

Dear GROMACS users, I read and followed Dr. Lemkul's tutorial on Free Energy Calculation on the webpage, http://www.mdtutorials.com/gmx/free_energy/index.html It is very helpful and easy to follow, but my ligand is protonated so the atomic charges in the topol.top are non-zero. The abov

Re: [gmx-users] How to reduce the penalty of small molecule from CGenFF

parameters? Thanks for your patient. Regards, Rolly On Thu, Mar 26, 2020 at 2:38 AM Justin Lemkul wrote: > > > On 3/25/20 12:52 PM, Rolly Ng wrote: > > Dear Gromacs Users, > > > > > > > > I am new to Gromacs and I followed the Protein-Ligand tutorial on

Re: [gmx-users] compile with intel compiler

Hi, I use the following combination with Intel PSXE. It works and your problem is likely related to the name of the Intel CXX compiler. source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64 source /opt/intel/impi/2018.4.274/bin64/mpivars.sh source /opt/intel/mkl/bin/mklvars.s

[gmx-users] How to reduce the penalty of small molecule from CGenFF

Dear Gromacs Users, I am new to Gromacs and I followed the Protein-Ligand tutorial on the following webpage, http://www.mdtutorials.com/gmx/complex/02_topology.html It works for the example JZ4 but as I changed to another molecule, the str file produced by the CGenFF server states very hig

[gmx-users] 回复: Gromacs 2020 fails to run adh_cubic_vsites

Dear Prof. Van der Spoel, Thank you for the quick reply. I just found that it works with 8, 16, 32, 64 and 128 threads but not 176 threads. Best, Rolly Ng -邮件原件- 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 David van der Spoel 发送时间: 2020年3月8日星期日 上午12:47 收件人: gmx-us

[gmx-users] Gromacs 2020 fails to run adh_cubic_vsites

adh_dodec_vsites failed at grompp. Could you please have a look at the following output log? Thanks, Rolly Ng PhD, Former Research Fellow, Department of Materials Science and Engineering City University of Hong Kong :-) GROMACS - gmx grompp, 2020-UNCHECKED

[gmx-users] Gromacs 2020 fails to run adh_cubic_vsites

adh_dodec_vsites failed at grompp. Could you please have a look at the following output log? Thanks, Rolly Ng PhD, Former Research Fellow, Department of Materials Science and Engineering City University of Hong Kong :-) GROMACS - gmx grompp, 2020-UNCHECKED