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AMBER Archive (2008)Subject: Re: AMBER: steered MD
From: Germain Vallverdu (germain.vallverdu_at_lcp.u-psud.fr)
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) ----------------------------------------------------------------------- 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 --
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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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