AMBER Archive (2008)

Subject: Re: AMBER: steered MD

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Wed Sep 10 2008 - 06:31:19 CDT

Apply all patches to amber please.
This is a problem solved by one of the bugfixes, related to the internal
setting for R4A by default.

Adrian

Germain Vallverdu wrote:
> 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)
>>> ----------------------------------------------------------------------- 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
>>> majordomo_at_scripps.edu
>>>
>>
>>
>>
>>
>
> --
> 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 majordomo_at_scripps.edu 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
-----------------------------------------------------------------------
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 majordomo_at_scripps.edu