From: Patrick Yee (pyee_at_nd.edu)
Date: Sun Apr 11 2010 - 14:07:52 CDT
Thanks for the help, Jerome.
I have one more quick question. I'm trying to find the PMF for a few
ion pairs in water, such as 1-ethyl-3-methylimidazolium (emim+) and
bis(trifluoromethylsulfonyl)imide (tf2n-). When I started my
simulations, I originally used distance-COM to compute the PMF. These
results didn't seem accurate since even after a 10ns simulation of 1fs
steps the PMF was very inconsistent. I then tried using an atom that
was an approximate "center" of the molecule (the carbon between the
nitrogens in the imidazolium and the nitrogen in the middle of the
tf2n) and just used distance instead of distance-COM to compute the
PMF. The results were drastically different between the distance and
distance-COMsimulations. Right now I'm trying Emim+ and Cl- since I
was thinking having just a Cl- ion instead of the larger tf2n- ion
might give better results.
For the TCL script ABF method for calculating the PMF, do you have any
suggestions about whether distance between specific atoms or
distance-COM would be better for my situations? Keep in mind that the
two molecules of interest are between 15 and 25 atoms. Are the results
for the PMF of the two solvated ions going to be accurate if only
distance between two selected atoms is used instead of distance-COM?
Finally, my simulation goes over the range 0 to 16 angstroms. Might
this be causing any problems considering the size of my molecules when
distance-COM is used?
I'm switching to NAMD 2.7b2 so I can use the collected variables
modules soon; are the comments you made about distance vs distance-COM
still true with colvars?
Thank you again and tell me if you want to see any input files I'm
using for my simulations.
Patrick Yee
On Wed, Mar 31, 2010 at 5:55 AM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> Hi Patrick,
>
> Unfortunately, you have encountered one of a few mysterious NAMD/Tcl
> bugs for which I do not know a fix or workaround. It seems to stem
> from some sort of memory corruption, and I have never been able to
> locate the faulty code either in the Tcl interpreter or in NAMD
> itself.
>
> Now, this would only happen when using the deprecated ABF code that
> was written for NAMD 2.6. In any case, switching to the newer
> "collective variables module" is strongly recommended. Are you sure
> that you are using the version of the tutorial which is currently
> online? That one should use the colvars module, and not suffer from
> Tcl-related limitations. Note that the text and files suffer from
> small inconsistencies (due to the transition from Tcl-ABF to colvars),
> but we are working hard right now to fix them. Hopefully, an updated
> version should go online very soon.
>
> Best,
> Jerome
>
>
> On 31 March 2010 00:10, Patrick Yee <pyee_at_nd.edu> wrote:
>> Hi NAMD users,
>>
>> I'm trying to find the PMF of an ion pair in water using the ABF
>> method. I'm having problems with jobs crashing when I try running ABF
>> simulations. The jobs seem to crash when I submit them to a node with
>> multiple cores. However, if I try running NAMD as a background process
>> on my workstation, the job runs fine, though it takes about 10 times
>> as long to complete. Does anyone have any suggestions or know
>> potential problems with what I'm doing?
>>
>> The abf.tcl script as well as the other ABF scripts are the same as
>> those found on http://www.ks.uiuc.edu/~char/tutorials/ABF/. The
>> equilibration of the system is fine, but adding the following causes
>> crashes when I submit jobs.
>>
>> source ../../Tutorial-ABF/abf-1.8/abf.tcl
>> abf coordinate distance-com
>> abf abf1 {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
>> 20 21 22 23 24 25}
>> abf abf2 {26 27 28 29 30 31 32 33 34 35 36 37 38 39 40}
>> abf ximin 0.05
>> abf ximax 15.95
>> abf dxi 0.2
>> abf fullSamples 4000
>> abf forceConst 12.0
>> abf writeXiFreq 10000
>> abf outfile abf_Bmim_Tf2N.abf
>>
>> The error I get in my log file is:
>>
>> TCL: can't use floating-point value as operand of "*"
>> FATAL ERROR: can't use floating-point value as operand of "*"
>> while executing
>> "expr {$retval + $term * $term}"
>> (procedure "veclength2" line 4)
>> invoked from within
>> "veclength2 $v"
>> (procedure "veclength" line 2)
>> invoked from within
>> "veclength $dr"
>> (in namespace eval "::ABF::ABFcoord" script line 4)
>> invoked from within
>> "namespace eval ABFcoord {
>>
>> set dr [vecsub $coords($group2) $coords($group1)]
>> set r [veclength $dr]
>> set nv [vecnorm $dr] ;# unity vector group1 -> ..."
>> (procedure "ABFapply" line 5)
>> invoked from within
>> "ABFapply $F"
>> (in namespace eval "::ABF" script line 87)
>> invoked from within
>> "namespace eval ::ABF {
>>
>> # First timestep : we don't have forces
>> if { $timestep == 0 } {
>>
>> # must not be equal to $timestep - 1
>> set timeStored -2
>> ..."
>> (procedure "calcforces" line 2)
>> invoked from within
>> "calcforces"
>> Stack Traceback:
>> [0] CmiAbort+0x4f [0x7eb405]
>> [1] _Z8NAMD_diePKc+0x62 [0x4b31e2]
>> [2] _ZN15GlobalMasterTcl9calculateEv+0x295 [0x65e723]
>> [3] _ZN12GlobalMaster11processDataEPiS0_P6VectorS2_S2_S0_S0_S2_S0_S0_S2_+0x71
>> [0x6524cd]
>> [4] _ZN18GlobalMasterServer11callClientsEv+0x43e [0x6564aa]
>> [5] _ZN18GlobalMasterServer8recvDataEP20ComputeGlobalDataMsg+0x6f7 [0x655b1b]
>> [6] _ZN10ComputeMgr21recvComputeGlobalDataEP20ComputeGlobalDataMsg+0x12
>> [0x52039a]
>> [7] _ZN18CkIndex_ComputeMgr48_call_recvComputeGlobalData_ComputeGlobalDataMsgEPvP10ComputeMgr+0xf
>> [0x520385]
>> [8] CkDeliverMessageFree+0x21 [0x786a6b]
>> [9] _Z15_processHandlerPvP11CkCoreState+0x455 [0x786075]
>> [10] CsdScheduleForever+0xa2 [0x7f18a2]
>> [11] CsdScheduler+0x1c [0x7f14a0]
>> [12] _ZN7BackEnd7suspendEv+0xb [0x4bab01]
>> [13] _ZN9ScriptTcl3runEPc+0x15b [0x6fbae5]
>> [14] main+0x21b [0x4b69c3]
>> [15] __libc_start_main+0xf4 [0x32b121d994]
>> [16] _ZNSt8ios_base4InitD1Ev+0x3a [0x4b2b5a]
>>
>>
>
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