VMD-L Mailing List

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Mon May 11 2009 - 12:29:37 CDT

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
>>>>