VMD-L Mailing List
From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Aug 01 2008 - 08:24:36 CDT
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Hi Alan,
I tried a test similar to what you're doing, but I get the expected
difference in electrostatic energy with and without 1-4scaling set:
petefred_at_algiers ~/vmdwork/plugins/namdenergy =) $ namd2 namd-temp.namd
| grep ^ENERGY:
ENERGY: 0 126.2869 269.3353 419.3776
0.0000 -23272.6906 2774.5828 0.0000
0.0000 0.0000 -19683.1080 0.0000
-19325.0163 -19325.0163 0.0000
petefred_at_algiers ~/vmdwork/plugins/namdenergy =) $ namd2
namd-temp-noamb.namd | grep ^ENERGY:
ENERGY: 0 126.2869 269.3353 419.3776
0.0000 -22741.4070 2774.5828 0.0000
0.0000 0.0000 -19151.8244 0.0000
-18793.6619 -18793.6619 0.0000
petefred_at_algiers ~/vmdwork/plugins/namdenergy =) $ diff namd-temp.namd
namd-temp-noamb.namd
16,17c16,17
< 1-4scaling 0.833333
< scnb 2
--- > #1-4scaling 0.833333 > #scnb 2 petefred_at_algiers ~/vmdwork/plugins/namdenergy =( $ If you just test a pair of config files with/without this setting outside of namdenergy, do things work ok for you? Best, Peter Alan wrote: > Thanks Peter. > > Pretty odd I know. > > And yes, I am sure my modified namdenergy.tcl is working because it > gives error if put a wrong instruction. Besides, if you see the log > files, you can clearly see 1-4scaling 0.8333 in one and 1.0 in the > other. And to be completely sure, I was restarting VMD between tests, > so it would source the modified file. > > I will test you code. But I am starting to think it can be NAMD the > culprit. Thanks a lot. > > Cheers, > Alan > > On Fri, Aug 1, 2008 at 5:59 AM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote: > >> Hi Alan, >> odd... this should certainly work. This sounds silly, but are you sure >> you're modifying the copy of namdenergy.tcl that's part of the installation >> you're using? If so, could you try sourcing this tcl file prior to opening >> the namdenergy gui in a new vmd session? >> I'm attaching the modified version of namdenergy which is now in cvs, which >> should hopefully be more convenient for all users. >> >> Please let me know if sourcing the modified script still doesn't help. >> >> Peter >> >> Alan wrote: >> >>> Hi Peter, >>> >>> Thanks for your reply. >>> >>> First I ran namdenergy GUI. Then I modified >>> vmd/plugins/noarch/tcl/namdenergy1.2/namdenergy.tcl and included: >>> >>> puts $namdconf "exclude\t\t\t scaled1-4" >>> puts $namdconf "1-4scaling\t\t\t 0.833333" <---- added >>> puts $namdconf "outputname\t\t ${jobname}-temp" >>> >>> Then, open vmd, ran namdenergy GUI with same set up (putting 'namd2' >>> in 'Temp File Prefix' and 'Output File' 'abc2.txt'). >>> >>> I am attaching a zip file with files generated by debug option. >>> >>> Summarising, although log files are different about '1-4scaling', the >>> rest and abc.txt and abc2.txt are identical. >>> >>> I am using latest version of Namd (2.6) and VMD (1.8.6) for Mac intel. >>> >>> I hope you can tell me what's going on here. >>> >>> Many thanks in advance. >>> Alan >>> >>> >>> On Thu, Jul 31, 2008 at 7:15 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> >>> wrote: >>> >>> >>>> Hi Alan, >>>> could you describe how you used namdenergy after you ran with the debug >>>> option and modified namd-temp.namd? Did you try to run it through the gui >>>> again or do it externally? I'm trying to verify that you didn't do >>>> anything >>>> to cause it to *re*write the .conf file prior to running namd. >>>> BTW, I've modified the version of namdenergy in cvs to automatically set >>>> 1-4scaling and sncb appropriately if you're using amber parameters, which >>>> should make life easier. >>>> Best, >>>> Peter >>>> >>>> Alan wrote: >>>> >>>> >>>>> Dears, >>>>> >>>>> I use NAMD for carrying on a simulation with amber99 ff. >>>>> >>>>> The I open it in VMD: >>>>> >>>>> vmd -parm7 ComplexAmber.prmtop -rst7 ComplexAmber.inpcrd run_namd.dcd >>>>> >>>>> and call namdenergy (dry-run) with debug option so I can modify >>>>> namd-temp.namd file. >>>>> >>>>> What I don't understand is why if I add and set 1-4scaling to 0.5, >>>>> 0.8333, 1 or whatever, the plot is exactly the same. I mean, if I run >>>>> a simulation with NAMD using amber input files I know that I have to >>>>> set 1-4scaling to 0.8333, but with namdenergy it seems to be ignored. >>>>> >>>>> I know that namdenergy will call NAMD to calculate energies all again >>>>> for a given simulation (among other reasons to unscramble PME), but I >>>>> don't realise why parameter "1-4scaling" is not taken in account. How >>>>> do I know that my vdw energies are correct according to amber >>>>> approach? >>>>> >>>>> Many thanks in advance. >>>>> >>>>> Alan >>>>> >>>>> >>>>> >>>>> >>> >>> >>> > > > > -- > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate > Department of Biochemistry, University of Cambridge. > 80 Tennis Court Road, Cambridge CB2 1GA, UK. > >>> http://www.bio.cam.ac.uk/~awd28<< >>>
- Next message: Axel Kohlmeyer: "Re: ionize with VMD a TOP file"
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- In reply to: Alan: "Re: namdenergy and simulation with amber ff"
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