Hi,
I think seeing your input for minimization could also be helpful.
Take a look at your trajectory if bubbles form during the heat-up process.
How did you solvate your system?
Try the following solvation process in leap:
"solvateoct mol TIP3PBOX 10 0.4"
see if that improves your minimization and warm-up processes..
Also, looking at your input that you sent, here are a few comments:
try using the following parameters in your input :
dt=0.002,
cut=9,
gamma_ln=10,
vlimit=5,
hope that helps,
regards,
jenk
Rachel <comeonsos.googlemail.com> wrote: Dear all,
I have a problem after minimization when I tried to heat up my system, this is my how I did the heating up:
#######################################################
MD with res on the protein
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0 ,
ntt = 3,
gamma_ln = 1.0,
nstlim = 20000, dt = 0.0005,
ntpr = 100, ntwx = 100, ntwr = 1000
/
Keep protein fixed with weak restraints
10.0
RES 1 791
END
END
#############################################################
When I use dt > 0.5fs (I tried dt=0.001, 0.0009, 0.0008, 0.0007, 0.0006), I got the error message like this:
##############################################################
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -218706.4292 EKtot = 0.0000 EPtot = -218706.4292
BOND = 402.6962 ANGLE = 2165.9364 DIHED = 6766.3301
1-4 NB = 2505.1240 1-4 EEL = 34266.4936 VDWAALS = 26154.1679
EELEC = -290967.1774 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.8028E-04
------------------------------------------------------------------------------
vlimit exceeded for step 0 ; vmax = Infinity
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 65751215812159
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
######################################################################
The I and J are different when I used different timestep.
As I kept decrease the timestep to 0.5fs, I got different error message:
######################################################################
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -218706.4292 EKtot = 0.0000 EPtot = -218706.4292
BOND = 402.6962 ANGLE = 2165.9364 DIHED = 6766.3301
1-4 NB = 2505.1240 1-4 EEL = 34266.4936 VDWAALS = 26154.1679
EELEC = -290967.1774 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.8028E-04
------------------------------------------------------------------------------
vlimit exceeded for step 0 ; vmax = Infinity
Coordinate resetting (SHAKE) was not accomplished
within 3000 iterations
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
#########################################################################
And if I kept decrease the timestep, I got the same message as above.
Also I have tried to change temp0 to smaller value (like 50), still I had the same problem.
I am not whether this is relevant, I have treated some of my atoms (hydrogen atoms) as extra-points as suggested by David Case, and I have such lines in my MD output:
########################################################################### 5. REFERENCE ATOM COORDINATES
----- READING GROUP 1; TITLE:
Keep protein fixed with weak restraints
GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
GRP 1 RES 1 TO 791
Number of atoms in this group = 12156
----- END OF GROUP READ -----
| EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 49969 0
| EXTRA_PTS, trim_bonds: num bonds AFTER trim = 49969 0
| EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 6328 0
| EXTRA_PTS, trim_bonds: num bonds AFTER trim = 6328 0
| EXTRA_PTS, trim_theta: num angle BEFORE trim = 13725 0
| EXTRA_PTS, trim_theta: num angle AFTER trim = 13725 0
| EXTRA_PTS, trim_theta: num angle BEFORE trim = 8660 0
| EXTRA_PTS, trim_theta: num angle AFTER trim = 8660 0
| EXTRA_PTS, trim_phi: num diheds BEFORE trim = 25765 0
| EXTRA_PTS, trim_phi: num diheds AFTER trim = 25765 0
| EXTRA_PTS, trim_phi: num diheds BEFORE trim = 16154 0
| EXTRA_PTS, trim_phi: num diheds AFTER trim = 16154 0
########################################################################
Does anyone know how to solve this problem? any suggestion is so much appreciated. Thank you in advance.
Best regards,
Rachel
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Received on Sun Dec 03 2006 - 06:08:09 PST
