[gmx-users] Potential energy reported by gmx energy command

[David van der Spoel]

Den 2018-07-04 kl. 11:19, skrev atb files:
> Thanks Prof. David, now my energies are making some sense and they are following the trend that, with increase in particle number RMSD decreases by (N)^1/2 for LJ fluid. If -nmol option is available, which may be used to calculate per particle averages, why default unit of "KJ/mol" has been used, which now looks very confusing. Please help Yogi ---- 

Because we typically simulation mixtures, e.g. 100 methanol and 100 
water or 1 protein in water. Then we can not decompose into molecules 
any more.




On Fri, 29 Jun 2018 01:31:47 +0530 David van der Spoel 
<spoel at xray.bmc.uu.se> wrote ---- Den 2018-06-28 kl. 09:03, skrev atb 
files: > Hello experts, I did a LJ particles simulation, where I 
simulated two systems, 100 particle and 400 particle. For 100 particles 
energy is: Energy                      Average   Err.Est.       RMSD  
Tot-Drift 
------------------------------------------------------------------------------- 
Potential                  0.126288      0.029   0.615731 -0.0324041  
(kJ/mol) Kinetic En.                 337.039       0.24    27.6568   
0.443176  (kJ/mol) Total Energy                337.165       0.22    
27.6615   0.410771  (kJ/mol) For 400 particle energy is: 
Energy                      Average   Err.Est.       RMSD  Tot-Drift 
------------------------------------------------------------------------------- 
Potential                  0.502517      0.042    1.34584   0.220501  
(kJ/mol) Kinetic En.                    1359       0.82    56.1468   
-1.24836  (kJ/mol) Total Energy                 1359.5       0.78    
56.1548   -1.02787  (kJ/mol) Since both systems have exact same 
operating conditions, only particle number has been changed, the per 
particle energy should be same, right? Here I see the energies has 
become 4 times in the second case. Then what is meaning of reporting 
energies in "KJ/mol" ? There is nothing like my system is not fully 
equilibrated, I have thoroughly checked, the both systems are well 
equilibrated. Please help in understanding these energies. Thank you > 
gmx energy does not know what your system is composed of. However the 
-nmol 400 flag may help. -- David van der Spoel, Ph.D., Professor of 
Biology Head of Department, Cell & Molecular Biology, Uppsala 
University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. 
http://www.icm.uu.se -- 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-request at gromacs.org.
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se