[gmx-users] friction constant for free energy calculation

Dear gmx users, I was trying to calculate free energy. I’m confused about setting the appropriate value for friction constant (= 1/tau-t). In gmx manual, a value of 0.5 ps-1 (tau-t = 2.0 ps) was suggested but 1.0 ps-1 (tau-t = 1.0 ps) was used in Justin’s tutorial. How much the results are

[gmx-users] Question about nsttcouple

Thank you for reply [ Input values in mdp file ] nstlist = 10 nsttcouple = -1 After gmx mdrun, ‘nstlist’ is automatically changed from 10 to 50. I expected that both ‘nstlist’ and ‘nsttcouple’ would be changed to 50, because ‘nsttcouple=-1’ means ‘nsttcouple=nstlist’. But, nstlist =50 and

[gmx-users] Question about nsttcouple

Dear gmx users, In gromacs manual, “nsttcouple: The default value of -1 sets nsttcouple equal to nstlist, unless nstlist <=0, then a value of 10 is used.” When I did grompp with the following mdp options, nstlist = 20 tcoupl = berendsen nsttcouple = -1 tau-t = 0.1 I got a warning

[gmx-users] angle/distance/position restraints in alchemical free energy calculation

I want to apply distance or angle restraints between any atoms of protein and any atoms of ligand to maintain the initial binding mode of ligand in the protein when non-bonded interactions entirely turned off. As described in figure 1 from the article (http

[gmx-users] angle/distance/position restraints in alchemical free energy calculation

I want to do it using gromacs. Is there any way to control those restraints (except dihedral angle) in gromacs? -- 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

[gmx-users] angle/distance/position restraints in alchemical free energy calculation

Dear gmx user, I’m studying about alchemical free energy calculation. I have been read some articles about restraints during free energy calculation, they referred the procedure in the article (http://pubs.acs.org/doi/pdf/10.1021/jp0217839). I tried to search mailing list, but still I couldn’t

[gmx-users] problem about installing the latest version of MOPAC

In PDF manual (GROMACS_2016.4), it is mentiond. “ The current version of GROMACS provides interfaces to several popular Quantum Chemistry packages (MOPAC, GAMESS-UK ….. “ Please let me know if I missed anything. Thanks. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] problem about installing the latest version of MOPAC

Dear gmx users, I’m trying to install MOPAC 2016 and GROMACS_2016.4 for QM/MM calculation. I have installed MOPAC, but it gives the following error when I configure “-DGMX_QMMM_PROGRAM=mopac” and then execute make command. [100%] [100%] Building CXX object

[gmx-users] problem about installing the latest version of MOPAC

Dear gmx users, I’m trying to install MOPAC 2016 and GROMACS_2016.4 for QM/MM calculation. I have installed MOPAC, but it gives the following error when I configure “-DGMX_QMMM_PROGRAM=mopac” and then execute make command. So how to set-up the latest version of MOPAC? Is it possible to use

[gmx-users] problem with dihedral restraints in gromacs 5.1.4.

Hello, I have tried to introduce dihedral restraints in gromacs 5.1.4. I modified topology file and mdp file as following:   In my topology file, #ifdef DIHRE [ dihedral_restraints ] ; ai  aj  ak  al   type   phi   dphi   kfac    7   8  9   10 1  180   0  100    7   8  9   14 1 

[gmx-users] How do I calculate the difference between two energy values?

Dear GROMACS users, I have been studying free energy calculation in Justin tutorial. I performed VDW decoupling and coulomb decoupling simulations separately. I obtained the free energy values for each simulation using gmx bar. coulomb decoupling simulation = 60.88 +/- 0.23 kJ/mol VDW

Re: [gmx-users] Histogram result in free energy calculation

.. Recently the server was fixed. So the following link is working now: http://bio.gnu.ac.kr/~chip/ Please give me any command to solve this problem. Regards, 2015-07-16 16:02 GMT+09:00 minky son minky0...@gmail.com: Dear GROMACS users. I have been studying free energy calculation in Justin

[gmx-users] Histogram result in free energy calculation

Dear GROMACS users. I have been studying free energy calculation in Justin tutorial. But, I got a somewhat different histogram result compared to the result in Justin tutorial. I uploaded my result files at the following link: http://bio.gnu.ac.kr/~chip/ I don't know why the result is