VMD-L Mailing List

From: Alan (alanwilter_at_gmail.com)
Date: Fri Aug 01 2008 - 02:05:23 CDT

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<<