Fwd: RAMD Setting parameter TclForces from script failed

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Mar 28 2011 - 15:37:24 CDT

I beg pardon again. My .bashrc contains

# For RAMD in NAMD
source /usr/local/namd_2.8nb/lib/ramd/scripts/ramd-4.1.tcl

In turn, the ramd portion of namd conf file, which come after the
"run" command, contains again

#*** Random Acceleration Molecular Dynamics
*************************************

source /usr/local/namd_2.8nb/lib/ramd/scripts/ramd-4.1.tcl

Does that result in having "tclforces on" after the "run" command?
I'll try to delete the second source.

f.

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Mon, Mar 28, 2011 at 10:19 PM
Subject: Fwd: namd-l: RAMD Setting parameter TclForces from script failed
To: Jim Phillips <jim_at_ks.uiuc.edu>, "Cojocaru,Vlad"
<vlad.cojocaru_at_mpi-muenster.mpg.de>, NAMD <namd-l_at_ks.uiuc.edu>

Sorry I forgot both Vlad and the list.

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Mon, Mar 28, 2011 at 10:17 PM
Subject: Re: namd-l: RAMD Setting parameter TclForces from script failed
To: Jim Phillips <jim_at_ks.uiuc.edu>

On Mon, Mar 28, 2011 at 9:33 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>
> It looks like you have "tclForces on" after run or minimize in your config
> file, so possibly your tclForces script was not active during the RAMD run
> at all.

Hi  Jim:
Yes, "tclforces on" is in the sourced ramd script, which comes after
the "run" command in namd conf file.  I had checked that against namd
2.7 with external namd: there was the same order of statements.

Now, if "tclforces on" is located in namd conf file, at the top:

# forcefield
paratypecharmm on
parameters ./par_all27_prot_lipid.prm
parameters ./AP1.r.prm
tclForces on

the error is:

Info: Configuration file is ramd_acc-03.conf
Info: Working in the current directory
/home/francesco/work_hasic1a_GLUP_ASPP_allHSP_S-S/9.ramd_04-1.1
TCL: Suspending until startup complete.
ERROR: 'tclForcesScript' is a required configuration option
ERROR:   when 'tclForces' is set
ERROR: tclForcesScript defines:   Tcl script for global forces
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE

Where should "tclforces on" be now located?

thanks
francesco

>
> -Jim
>
> On Mon, 28 Mar 2011, Francesco Pietra wrote:
>
>> Hi:
>> I carried out a trial RAMD simulation with namd.2.8 (from binary
>> Linux64) charmmff for a protein-organic-ligand in a lipidic membrane.
>>
>> The simulation ended correctly at the bare 100 chosen steps, the
>> ligand did not move - as expected from 1000 steps  acc 0.3 ts 1fs.
>> Everything seems OK except the error below. I vaguely remember that
>> Vlad warned me in the past to compile namd in order that ramd exists
>> correctly. Was that the same errior message or anything new about
>> which I should now care?
>>
>> thanks
>> francesco pietra
>>
>> **************************
>>
>> ENERGY:    1000     10573.6218     17958.2104      9301.2411
>> 779.3272        -763083.0117     55270.6864         0.0000
>> 1.9652    144208.1552        -524989.8044       308.8680
>> -669197.9596   -524727.0908       309.0692           -173.1971
>> -32.1881   2166358.3052       -35.4825       -31.7813
>>
>> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000
>> WRITING COORDINATES TO DCD FILE AT STEP 1000
>> WRITING COORDINATES TO RESTART FILE AT STEP 1000
>> FINISHED WRITING RESTART COORDINATES
>> The last position output (seq=1000) takes 0.134 seconds, 744.610 MB of
>> memory in use
>> WRITING VELOCITIES TO RESTART FILE AT STEP 1000
>> FINISHED WRITING RESTART VELOCITIES
>> The last velocity output (seq=1000) takes 0.021 seconds, 744.609 MB of
>> memory in use
>> TCL: Setting parameter TclForces to on
>> FATAL ERROR: Setting parameter TclForces from script failed!
>>
>> FATAL ERROR: Setting parameter TclForces from script failed!
>>
>> ------------- Processor 1 Exiting: Called CmiAbort ------------
>> Reason: FATAL ERROR: Setting parameter TclForces from script failed!
>>
>>
>> FATAL ERROR: Setting parameter TclForces from script failed!
>>
>> ------------- Processor 3 Exiting: Called CmiAbort ------------
>> Reason: FATAL ERROR: Setting parameter TclForces from script failed!
>>
>>
>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>> Reason: FATAL ERROR: Setting parameter TclForces from script failed!
>>
>>
>> FATAL ERROR: Setting parameter TclForces from script failed!
>>
>> ------------- Processor 2 Exiting: Called CmiAbort ------------
>> Reason: FATAL ERROR: Setting parameter TclForces from script failed!
>> **************************
>>
>

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