From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Thu May 04 2006 - 10:02:27 CDT
Actually, the line "set temperature 300" is a tcl command line which sets
the variable "temperature" to 300. Nothing to do with setting the
velocities at that point. The two lines conflicting are likely:
You should comment out the second one (which is the actual command
setting a Gaussian distribution of velocities).
If you eliminate the line "set temperature $temperature", then you will
have troubles with the Langevin temperature control or any other place where
the variable $temperature is being used.
On Thu, 4 May 2006, Marc Q. Ma wrote:
> you need to comment out either line (binVelocities, set temperature). when a
> temperature value is entered in the config, NAMD uses it to generate a
> velocity for each atom -- following a Gaussian distribution, together gives
> an instantaneous kinetic temperature of the set value. you can not do both.
> On May 4, 2006, at 7:44 AM, Osman Yogurtcu wrote:
>> I am getting an error while continuing a NAMD run after the minimization,
>> which says "Cannot specify both an initial temperature and a velocity
>> file". Inside my .conf file I have these lines...
>> structure ../common/1BFT_A_wb_ion.psf
>> coordinates ../common/1BFT_A_wb_ion.pdb
>> binCoordinates ../mini/res.coor
>> binVelocities ../mini/res.vel
>> extendedSystem ../mini/res.xsc
>> set temperature 300
>> The error suggests that I should comment out the temperature. However, my
>> friends in the lab, although they have the exact code, do not receive any
>> error. What am I missing? Is there something wrong with my minimization?
>> Osman Yogurtcu
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