Re: AMBER: steered MD

From: Germain Vallverdu <germain.vallverdu.lcp.u-psud.fr>
Date: Wed, 10 Sep 2008 13:17:10 +0200

This is the dist.RST file :

# change phi de r2=0 a r2a = 180 degre
&rst iat=21,22,24,25, r2=0., rk2=5000., r2a=180.,  /

I tried with that :

# change phi de r2=0 a r2a = 180 degre
&rst iat=21,22,24,25, r2=0., rk2=5000., r2a=180., r4a=360.,  /

But it does not work :

Here is the input file (mdin) :

steered MD sur phi
&cntrl
 nstlim=50000,  dt=0.001,
 irest=0,  ntx=1, iwrap=1, ig=100908
 ntpr=1000, ntwr=1000, ntwx=100,
 tempi=300.0, temp0=300.0, ntt=3, gamma_ln=1.0,
 ntb=2, pres0=1.0, ntp=1, taup=2.0,
 ntc=2, ntf=2,
 cut=10.0,
 jar=1,
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END',   /
DISANG=steeredcoord
DUMPAVE=phi_vs_t
LISTIN=POUT
LISTOUT=POUT

Thanks

Germain



Carlos Simmerling a écrit :

can you show us the dist.RST file?

On Wed, Sep 10, 2008 at 6:26 AM, Germain Vallverdu
<germain.vallverdu.lcp.u-psud.fr> wrote:
  

Hello AMBER !

I am trying to do a steered MD with the following dist.RST file :

# change phi de r2=0 a r2a = 180 degre
&rst iat=21,22,24,25, r2=0., rk2=5000., r2a=180.,  /

But the run stops at the beginning with this error message :

******
 CA2 (   21)-CB2 (   22)-CG2 (   24)-CD1 (   25)    NSTEP1=     0 NSTEP2=
50000
R1 =-100.000 R2 =   0.000 R3 =   0.000 R4 = 100.000 RK2 =5000.000 RK3 =
5000.000
R1A=-100.000 R2A= 180.000 R3A= 180.000 R4A= 100.000 RK2A=   0.000 RK3A=
0.000
 Rcurr:   -0.131  Rcurr-(R2+R3)/2:    0.131  MIN(Rcurr-R2,Rcurr-R3):
0.131
 ERROR: r1 -> r4 (and r1a -> r4a) must be monotonically increasing;
Offending restraint:
******
 CA2 (   21)-CB2 (   22)-CG2 (   24)-CD1 (   25)    NSTEP1=     0 NSTEP2=
50000
R1 =-100.000 R2 =   0.000 R3 =   0.000 R4 = 100.000 RK2 =5000.000 RK3 =
5000.000
R1A=-100.000 R2A= 180.000 R3A= 180.000 R4A= 100.000 RK2A=   0.000 RK3A=
0.000

I tried to defined r4a into the dist.RST file but it does not work.

As you saw my coordinate is a dihedral angle and r4a is too small.

Thanks

Germain


--
Germain Vallverdu
Laboratoire de Chimie Physique
Université Paris Sud 11
germain.vallverdu.lcp.u-psud.fr
01 69 15 30 38 / 06 88 59 08 87
Chacun de nous a son étoile. Suivons la en nous félicitant de la voir chaque
jour un peu plus loin ! (V. Grignard)
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----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to majordomo.scripps.edu Received on Thu Sep 11 2008 - 08:40:57 PDT