AMBER Archive (2008)

Subject: Re: AMBER: steered MD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Sep 10 2008 - 06:23:51 CDT

it might help to explicitly define all of the r1/r2/r3/r4 and
r1a/r2a/r3a/r4a. you also need ifvari if you want to change the
restraints. in fact, I don't really see how either of these entries
could give the mdout data you sent before.
what do you mean by "it does not work"? please give the error message
or response from sander.

2008/9/10 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_at_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_at_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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>
>
> --
> Germain Vallverdu
> Laboratoire de Chimie Physique
> Université Paris Sud 11
> germain.vallverdu_at_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_at_scripps.edu To unsubscribe,
> send "unsubscribe amber" (in the *body* of the email) to
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Professor, Department of Chemistry
CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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