VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Aug 01 2008 - 08:24:36 CDT

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<<
>>>