Re: question on pairinteraction

From: Peter Freddolino (
Date: Sun Feb 26 2006 - 11:25:50 CST

Dear Longzhu,
there are some parameters in NAMD which cannot be changed once a run
begins; pairinteraction is one of them (others include things like
annealing options). So the problem here is that you've already run
100000 steps, and then try to turn on pair interactions after that.
Things should work fine if you just split these up into separate runs
and then use the restart files from the equilibration to start your pair
interaction run.

Also, you may want to make sure that the "Pair Interaction parameters"
line is commented out; it probably was in your actual file but does not
appear to be in the email.


Longzhu Shen wrote:

>Dear All,
>I am trying to calculate the interaction energy with namd. But it returned the
>following errors:
>FATAL ERROR: Setting parameter pairinteraction from script failed!
>The partial configuration file is:
>langevinPiston on
>run 100000 ;#
>output ${export}/equil_Pr
>constraintScaling 0
>Pair Interaction parameters
>pairinteraction on
>pairinteractionfile pair_ref.pdb
>pairinteractioncol B
>pairinteractiongroup1 1
>pairinteractiongroup2 2
>run 500000 ;#
>output ${export}/equil
>I was wondering how to tackle this problem. Your kind help would be highly
>Longzhu Shen

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