Re: NAMDenergy

From: Holly Freedman (
Date: Wed Jul 05 2006 - 12:12:04 CDT

I've gotten some really helpful responses from users, after having spent
much time tryng to figure this out on my own. I'm sorry to bother your
list if it wasn't meant for this, but I was trying to use the VMD gui to
design input for NAMD, so I didn't relaize that the message should have
been sent to the VMD list.


>> Maybe this person did that already...
>> Richard
> Maybe they did.... but all the evidence they gave me was they were
> off-topic, they knew they were off-topic, they were trying to use a tool
> for molecular visualization for "energy analysis", and they appeared not
> to understand how to import a trajectory into VMD (I can't be sure what
> they mean by "this gui", however) - when that topic has a section in the
> VMD user's guide and is basic usage technique.
> 424 other NAMD-L subscribers ignored them for 10 hours, and for six hours
> more before your reply... all I did was politely point them towards
> avenues of inquiry that were more likely to be fruitful. I think it would
> be out-of-line to imply that I acted inappropriately in this case. I have
> no obligation to be exaggeratedly friendly, or to assume a certain level
> of knowledge in the other subscribers, and I did act to help them.
> Mark
>> ----- Original Message ----
>> From: Mark Abraham <>
>> To:
>> Sent: Tuesday, July 4, 2006 11:51:44 PM
>> Subject: Re: namd-l: NAMDenergy
>>> Hi NAMD help,
>>> I'm confused because the VMD gui for energy analysis seems to be able
>>> to
>>> open as input only psf files, but it looks like it's designed to
>>> analyze
>>> trajectories as well. Is it possible to open a trajectory file as
>>> input
>>> in this gui, and if so could you please tell me how?
>> Perhaps you should try reading the VMD documentation, or asking the
>> VMD-L
>> mailing list.
>> Mark

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