RE: Temperature reassignment problem

From: Kamp, Marc vander (Marc.vanderKamp_at_wur.nl)
Date: Wed Jun 23 2004 - 05:13:34 CDT

A few days ago I posted a problem I had with temperature reassignment. My problem was (see previous posting in this thread) that temperatures from the first simulation step on were reassigned at the value I had set for 'reassignHold'.
I did'nt take the time to test what might cause the problem before, but now I did.
The problem was that I had set 'firsttimestep 4000', because I wanted to continue counting after the 4000 steps minimization I did on the same system before.
Apparently, the temperature reassignment-parameters begin counting at timestep zero, it doesn't take account for the fact the simulation starts at the timestep specified by 'firsttimestep'. Therefore, the temperature specified in reassignHold was already reached at the start of the simulation. Changing the firsttimestep to zero solves this problem, as can be expected of course.
 
Maybe this could be changed in a next version of NAMD, so it will be possible to do controlled heating without having to set the firsttimestep to zero? (Might also be usefull for doing SA after equilibration of the system.)
 
Regards,
Marc
 
 
 

        -----Original Message-----
        From: owner-namd-l_at_ks.uiuc.edu on behalf of Kamp, Marc vander
        Sent: Mon 21-6-2004 11:19
        To: namd-l_at_ks.uiuc.edu
        Cc:
        Subject: namd-l: Temperature reassignment problem
        
        

        Dear all,
        
        I would like to gradually heat my system after minimization. I tried to do this by the following settings in the conf. file (in the execution-part of the script, because I would like to do different MD-phases (with/without constraints) in 1 go):
        
        # Heat to $temperature with 25K every 0.5 ps (takes 5 ps to reach 300K)
        reassignTemp 50
        reassignFreq 250
        reassignIncr 25
        reassignHold $temperature
        
        When I look into the log-file however, I see that the temperature is reassigned to 300 K (which is the value of $temperature, set by: 'set temperature 300') instead of 50, 75, 100 and so on.
        What could be the problem?
        
        Thanks in advance,
        Marc
        
        Here's the output of ' grep "REASSIGNING VELOCITIES" test_eq_cpt2.log ' :
        REASSIGNING VELOCITIES AT STEP 4000 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 4250 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 4500 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 4750 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 5000 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 5250 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 5500 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 5750 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 6000 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 6250 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 6500 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 6750 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 7000 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 7250 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 7500 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 7750 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 8000 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 8250 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 8500 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 8750 TO 300 KELVIN.
        REASSIGNING VELOCITIES AT STEP 9000 TO 300 KELVIN.
        
        
        

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