From: PANAGIOTA KYRIAKOU (kyria008_at_gmail.com)
Date: Wed Jan 01 2014 - 18:17:40 CST
Hi there,
Thanks for your answer..
I thought the use of the commands reassignFreq, reassignTemp etc was
gradual heating. I just do not understand what I am doing wrong.
I had problems with the constrains so this is why I used 1fs.
Giota
Panagiota Kyriakou
Graduate Student
Dept. of Chemical Engineering and Materials Science
University of Minnesota
email: kyria008_at_umn.edu
On Wed, Jan 1, 2014 at 9:27 AM, Thomas Evangelidis <tevang3_at_gmail.com>wrote:
> Energy minimization is like dropping the temperature of the system to 0
> Kelvin. Therefore, in order to initialize velocities at 303 Kelvin you must
> first do the gradual heating from 0->303 K otherwise the system will blow
> up. Unlike GROMACS or AMBER, NAMD does not do the heating automatically.
> Replace "run 1000000" with something like:
>
> # Heating
> set HeatSteps 5
> set HeatMDsteps 1000
> for {set i 1} {$i <= $HeatSteps } { incr i } {
> set t [expr $temp*$i/$HeatSteps]; puts "Heat structure to $t K for
> $HeatMDsteps steps."
> reinitvels $t
> run $HeatMDsteps
> }
> reinitvels $temp
> run 1000000 ;# 1 ns at $temp Kelvin
>
>
> Also are you sure you want to use a timestep of 1 fs?
>
>
> On 31 December 2013 19:28, PANAGIOTA KYRIAKOU <kyria008_at_gmail.com> wrote:
>
>> Hello,
>>
>> I have been trying to equilibrate my system that consists of protein
>> embedded in a membrane and I get the following error:
>>
>> *TIMING: 500000 CPU: 9750.65, 0.021551/step Wall: 9750.65,
>> 0.021551/step, 0 hours remaining, 556.101562 MB of memory in use.*
>> *ETITLE: TS BOND ANGLE
>> DIHED IMPRP ELECT VDW
>> BOUNDARY MISC KINETIC TOTAL TEMP
>> POTENTIAL TOTAL3 TEMPAVG PRESSURE
>> GPRESSURE VOLUME PRESSAVG GPRESSAVG*
>> *ENERGY: 500000 48376.8664 114689
>> <8664%20%C2%A0%20%C2%A0114689>.7899 11643.7243 506.4399
>> -580965.4098 103191 <4098%20%C2%A0%20%C2%A0103191>.7767 0.0000
>> 246.2954 0.0000 -302310.5171 0.0000
>> -302310.5171 -302310.5171 0.0000 6488.4885
>> 6928.4046 1914140.8650 6488.4885 6928.4046*
>>
>> *WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 500000*
>> *WRITING COORDINATES TO DCD FILE AT STEP 500000*
>> *WRITING COORDINATES TO RESTART FILE AT STEP 500000*
>> *FINISHED WRITING RESTART COORDINATES*
>> *WRITING VELOCITIES TO RESTART FILE AT STEP 500000*
>> *FINISHED WRITING RESTART VELOCITIES*
>> *TCL: Writing to files with basename A_equil_1_min.*
>> *WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 500000*
>> *WRITING COORDINATES TO OUTPUT FILE AT STEP 500000*
>> *WRITING VELOCITIES TO OUTPUT FILE AT STEP 500000*
>> *TCL: Running for 1000000 steps*
>> *REASSIGNING VELOCITIES AT STEP 500000 TO 303.15 KELVIN.*
>> *colvars: Writing the state file "A_equil_1.restart.colvars.state".*
>> *colvars: Synchronizing (emptying the buffer of) trajectory file
>> "A_equil_1.colvars.traj".*
>> *ERROR: Constraint failure in RATTLE algorithm for atom 6522!*
>> *ERROR: Constraint failure; simulation has become unstable.*
>> *ERROR: Constraint failure in RATTLE algorithm for atom 13834!*
>> *ERROR: Constraint failure; simulation has become unstable.*
>> *ERROR: Constraint failure in RATTLE algorithm for atom 1812!*
>> *ERROR: Constraint failure; simulation has become unstable.*
>>
>> When I tried to fix it I realized that the Temperature increased from 0
>> to 312 K, instantly after minimization even though I am using temperature
>> reassignment. Here is my configuration file:
>>
>>
>> *#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#*
>> *# Custom variables*
>> *set temp 303.15 *
>>
>> *# inputs*
>> * structure ../A.psf ; *
>> * coordinates ../A.pdb ;*
>> * paraTypeCharmm on*
>> * parameters ../../common/topology/par_all36_prot_nomass.prm*
>> * parameters ../../common/topology/par_all36_water_ions.prm *
>> * parameters ../../common/topology/par_all36_lipid.prm *
>>
>>
>> * temperature $temp ;*
>> * # simulation parameters*
>> * outputname A_equil_1 ;*
>> * outputEnergies 1000 ;*
>> * outputTiming 1000 ;*
>> * xstFreq 10000 ;*
>> * dcdFreq 10000 ;*
>> * dcdUnitCell yes *
>> * binaryoutput on ;*
>> * restartfreq 10000 ;*
>> * seed 1369948321 ;*
>>
>> *# calculation parameters*
>> * exclude scaled1-4 ;*
>> * 1-4scaling 1.0 ;*
>> * switching on ;*
>> * switchDist 9 ;*
>> * cutoff 10 ;*
>> * pairlistdist 12 ; *
>> * stepsPerCycle 20 ;*
>> * rigidbonds all ;*
>> * vdwForceSwitching yes ;*
>> * timestep 1 ; *
>> * nonBondedFreq 1 ;*
>> * fullElectFrequency 1 ;*
>> * cellBasisVector1 139.65999603271484 00.00 00.00 ;*
>> * cellBasisVector2 00.00 140.35699462890625 00.00 ;*
>> * cellBasisVector3 00.00 00.00 97.64900207519531 ;*
>> * cellorigin -0.9953396916389465 4.457383155822754
>> 2.071026086807251 ;*
>> * wrapAll on ;*
>> * wrapWater on ;*
>> * wrapNearest off ;*
>>
>> *# PME*
>> * Pme on ;*
>> * PmeGridsizeX 144 ;*
>> * PmeGridsizeY 150 ;*
>> * PmeGridsizeZ 108 ;*
>>
>>
>> *# Control (need to be specified before runs) *
>> * useFlexibleCell yes ;*
>> * useGroupPressure yes ;*
>> * useConstantRatio yes ;*
>>
>> *# constant pressure*
>> * langevinPiston on*
>> * langevinPistonTarget 1.01325*
>> * langevinPistonPeriod 50.0*
>> * langevinPistonDecay 25.0*
>> * langevinPistonTemp $temp*
>>
>> * reassignFreq 1000 ;*
>> * reassignTemp 1 ;*
>> * reassignIncr 1 ;*
>> * reassignHold $temp ; *
>>
>> * colvars on*
>> * colvarsConfig ../restraints/A_equil_1.col *
>>
>>
>> *#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#*
>> * # EXECUTION*
>>
>> *#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#*
>> * minimize 500000*
>>
>> * run 1000000*
>>
>>
>> Do you know what could have caused the increase in the temperature?
>> I would appreciate your help so much,
>>
>> Giota
>>
>> Panagiota Kyriakou
>>
>> Graduate Student
>>
>> Dept. of Chemical Engineering and Materials Science
>>
>> University of Minnesota
>>
>>
>> email: kyria008_at_umn.edu
>>
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang_at_pharm.uoa.gr
>
> tevang3_at_gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
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