Ang: [gmx-users] Temp increase

[Peter Ahlström]

Dear Nguyen,

What you describe is a classical problem i MD-simulations, all inaccuraies tend to result in a raised temperature (which you take away more  efficiently but also more unphysically with a 
shorter coupling time.
Most probable reason is the treatment och charged groups. 
What cut-off radius do you use for electrostatic interactions?
Does you peptide contain any net charged groups (like -[COO^-] or -[NH_3^+]) or only dipoles characterized by partial charges?
Do you use a plain cut-off or a charge group cut-off for your dipoles? 
(If you use a charge-group cut-off for your dipoles and have no net charged groups your energy conservation will be much better).
This is probably discussed in the Gromacs manual.
(See also the answer by Bert de Groot)

Peter Ahlström
School of Engineering
University College of Borås
SE-501 90 Borås, Sweden
peter.ahlstrom at hb.se


<<< Nguyen Hoang Phuong <phuong at theochem.uni-frankfurt.de> 22/2 15:37   >>>

Dear Gromacs Users,

I have simulated the peptide in H2O. The simulation has been done
as the following:

1)Energy minimization with fixed peptide

2)simulating for 5ps with fixed peptide

dt    = 0.002
tau_p = 0.05
tau_t = 0.01

3)simulating for next 5ps without position constraining of peptide

dt    = 0.002
tau_p = 0.1
tau_t = 0.01

4)Long run:

if( tau_t = 0.1)  -->  I get the temperature shifted about +10K 
if( tau_t = 0.01) --> I get the right temperature 

(tau_p = 0.1, dt =0.002)

Any explaination is  appreciated.! Thanks you.

Phuong
------

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