VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon May 11 2009 - 12:37:07 CDT

Ah yes, that would do it.Thanks for letting me know. I'll have to add a
switch to let the user pick the exclusion type. I've always used a
tweaked version of namdenergy while analyzing CG trajectories.
Best,
Peter

BIN ZHANG wrote:
> Hi, peter:
>
> Thanks a lot for your reply.
> I finally figured out what the problem is. It's because I'm using the
> coarse grained model, however, the default value for "exclude" is
> "scaled1-4" in NAMDEnergy. ;-)
>
> Thanks,
> Bin
>
>
> On May 10, 2009, at 9:27 PM, Peter Freddolino wrote:
>
>> Hi Bin,
>> sorry for my slow reply; I was out of town.
>> As a first step, could you try running namdenergy with the -debug flag,
>> and then verify that the error occurs if you just run namd on the .namd
>> file generated in that directory? If it does, try adding "margin 10" to
>> the config file and run it again.
>>
>> The energy from -sel $sel1 $sel1 should be identical to -sel $sel1 in
>> your case, but it would be nice to know why you're getting the exclusion
>> count error.
>> Best,
>> Peter
>>
>> BIN ZHANG wrote:
>>> Hi, Peter:
>>>
>>> I'm using the official VMD 1.8.6 along with the namd2.6 for MacOSX, and
>>> I did include PME and the PBC info for the calculation. (I did NOT type
>>> them in the original email, sorry for the confusion).
>>>
>>> Thanks,
>>> Bin
>>>
>>>
>>> On May 7, 2009, at 8:45 PM, Peter Freddolino wrote:
>>>
>>>> Could you let us know what version of namd/vmd you're using? Also, if
>>>> you used periodic boundary conditions and PME in your simulation, you
>>>> should also do so for the postprocessing...
>>>> Best,
>>>> Peter
>>>>
>>>> BIN ZHANG wrote:
>>>>> Dear all:
>>>>>
>>>>> I met a quite peculiar error while using the NAMDEnergy plugin. I was
>>>>> trying to calculate the internal energy of a peptide, and using the
>>>>> following command,
>>>>>
>>>>> set sel1 [atomselect top "chain D"]
>>>>> namdenergy -nonb -sel $sel1
>>>>>
>>>>> I would get a error " bad global exclusion count".
>>>>> However, if I use :
>>>>> namdenergy -nonb -sel $sel1 $sel1.
>>>>> then everything seems to be working fine.
>>>>>
>>>>> Can anyone explain to me why is this happening? Assuming the second
>>>>> case
>>>>> is running correctly, would it twice as large as the first one?
>>>>>
>>>>> Thanks,
>>>>> Bin
>>>>>