From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Mar 28 2011 - 16:09:55 CDT
Having ramd-4.1.tcl sourced by .bashrc only, the required 200 steps
of simulation were completed as pure MD, followed by the error:
ENERGY: 200 10414.2894 18086.1558 9302.0913
742.3372 -762772.7609 55176.1438 0.0000
1.3552 144123.5647 -524926.8235 308.6868
-669050.3882 -524661.6394 308.8170 -144.4734
-49.9279 2165870.0634 -72.7250 -64.5812
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 200
WRITING COORDINATES TO DCD FILE AT STEP 200
WRITING COORDINATES TO RESTART FILE AT STEP 200
FINISHED WRITING RESTART COORDINATES
The last position output (seq=200) takes 0.136 seconds, 326.080 MB of
memory in use
WRITING VELOCITIES TO RESTART FILE AT STEP 200
FINISHED WRITING RESTART VELOCITIES
The last velocity output (seq=200) takes 0.023 seconds, 324.607 MB of
memory in use
TCL: wrong # args
FATAL ERROR: wrong # args
while executing
"ramd debugLevel 0 "
(file "ramd_acc-03.conf" line 92)
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: wrong # args
while executing
"ramd debugLevel 0 "
(file "ramd_acc-03.conf" line 92)
This is my namd conf file at the interface namd-ramd:
seed 15343
run 200
#############################################################
#*** Random Acceleration Molecular Dynamics
*************************************
# source /usr/local/namd_2.8nb/lib/ramd/scripts/ramd-4.1.tcl
#*** sources the wrapper script ramd-4.1.tcl;
#*** please change the directory '../scripts/' to '' ( the correct path );
#*** directory '' should contain the scripts: ramd-4.1.tcl,
ramd-4.1_script.tcl, and vectors.tcl
ramd debugLevel 0
#*** activates verbose output if set to something else than 0
ramd ramdSteps 50
#*** specifies the number of steps in 1 ramd stint;
#*** defaults to 50
ramd accel 0.3
#*** specifies the acceleration to be applied;
#*** defaults to 0.25 kcal/mol*A*amu
For some reasons the ramd part of namd conf file is not read, it does
not appear into the namd log file, unlike in my older ramd simulations
with namd. There, the log file showed :
Info: useSync: 1 useProxySync: 0
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
TCL: RAMD:
TCL: RAMD: -------------------------------------------------------------------
TCL: RAMD: Random Acceleration Molecular Dynamics Simulation version 4.1
TCL: RAMD: -------------------------------------------------------------------
TCL: RAMD:
TCL: RAMD: mdSteps = 0
TCL: RAMD: accel = 0.1
TCL: RAMD: ramdSeed = 627
I think to be confused enough at the moment not to be useful to myself
while annoying op
francesco
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On Mon, Mar 28, 2011 at 10:37 PM, Francesco Pietra
<chiendarret_at_gmail.com> wrote:
> 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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