From: Canal de Sebassen (thecromicusproductions_at_gmail.com)
Date: Fri Nov 15 2019 - 11:25:34 CST
I have another question about these simulations. I started running some
yesterday and:
1) initially some walkers do not start at all. I get messages like
colvars: Metadynamics bias "metadynamics1": failed to read the file
"metadynamics1.rep1.files.txt": will try again after 10000 steps.
and in the same step the walker reads the other replicas and ends with
colvars: Metadynamics bias "metadynamics1": reading the state of replica
"rep1" from file "".
colvars: Error: in reading state configuration for "metadynamics" bias
"metadynamics1" at position -1 in stream.
2) others, they run for a while but then give me a message
colvars: Error: in reading state configuration for "metadynamics" bias
"metadynamics1" at position -1 in stream.
FATAL ERROR: Error in the collective variables module: exiting.
3) in the end, I only get 3 walkers to work, with the other 9 I sent left
for dead. I'm running these simulations in my local cluster, with the
following code
#!/bin/bash
#$ -pe mpi-24 288 # Specify parallel environment and legal core size
#$ -q long # Specify queue
#$ -N Trial1 # Specify job name
TASK=0
cat $PE_HOSTFILE | while read -r line; do
host=`echo $line|cut -f1 -d" "|cut -f1 -d"."`
echo $host >> hostfile
done
hostfile="./hostfile"
while IFS= read -r host
do
let "TASK+=1"
/usr/kerberos/bin/rsh -F $host -n "uname -a; echo $TASK; cd XXXXXXXXX;
pwd; module load namd; mpirun -np 24 namd2 testres.rep$TASK.namd >
s$TASK.0.log ; exit" &
done < $hostfile
wait
rm ./hostfile
Am I doing something wrong? Currently the times of my colvars are
colvarsTrajFrequency 10000
metadynamics {
colvars d1 d2
useGrids on
hillWeight 0.05
newHillFrequency 10000
dumpFreeEnergyFile on
dumpPartialFreeEnergyFile on
saveFreeEnergyFile on
writeHillsTrajectory on
multipleReplicas yes
replicaID rep9
replicasRegistry replicas.registry.txt
replicaUpdateFrequency 10000
and my namd outputs are
numSteps 25000000
outputEnergies 10000
outputPressure 10000
outputTiming 10000
xstFreq 10000
dcdFreq 10000
restartFreq 10000
Thanks,
Sebastian
On Sat, Nov 9, 2019 at 8:03 PM Canal de Sebassen <
thecromicusproductions_at_gmail.com> wrote:
> Thanks for your reply, Giacomo. I'll take your suggestions into
> consideration when setting up the system.
>
> Regards,
>
> Sebastian
>
> On Thu, Nov 7, 2019 at 6:37 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hi Canal, first of all try upgrading to the latest NAMD nightly build.
>> Thanks to Jim's help, I added extra checks that make the input/output
>> functionality more robust (the same checks are used when writing the NAMD
>> restart files):
>> https://github.com/Colvars/colvars/pull/276
>> There is also an important bugfix in the output of the PMF (the restart
>> files are fine):
>> https://github.com/Colvars/colvars/pull/259
>>
>> About the exchange rate, on modern hardware optimal performance is around
>> few milliseconds/step, so 1000 steps is kind of short for a full cycle with
>> all replicas reading each others' files. Best to increase it by a factor
>> of 10 or more: I would have made its default value the same of the restart
>> frequency, but there is no telling how long that would be for each user's
>> input.
>>
>> Regarding the PMFs, nothing special is needed. Each replica will write
>> PMFs with the same contents (the PMF extracted from the shared bias), so
>> they will be equal minus the fluctuations arising from synchronization.
>> You are probably confused by the partial output files, which are triggered
>> by dumpPartialFreeEnergyFile (a flag that is off by default).
>>
>> Lastly, Gaussians 0.01 kcal/mol high added every 100 steps is quite a bit
>> of bias, and will be further multiplied by the number of replicas.
>>
>> Giacomo
>>
>> On Thu, Nov 7, 2019 at 6:06 PM Canal de Sebassen <
>> thecromicusproductions_at_gmail.com> wrote:
>>
>>> Hello,
>>>
>>> Say I run a metadynamics simulation with 10 walkers. I then get 10
>>> different pmf files. If my simulation was in 2D, how do I get a single
>>> energy landscape? Do I use abf_integrate?
>>>
>>> Also, what are some good practices when running these kind of
>>> simulations?
>>> I haven't found many examples. This is one my current colvars files. I
>>> plan to get about 1-5 microseconds of data. Is a replicaUpdateFrequency of
>>> 1000 too large? I tried with a smaller one but I get problems because some
>>> files of a replica cannot be found by another one (maybe due to lagging?).
>>>
>>> Thanks,
>>>
>>> Sebastian
>>>
>>> colvarsTrajFrequency 100
>>>
>>> colvar {
>>>
>>> name d1
>>>
>>> outputAppliedForce on
>>> width 0.5
>>>
>>> lowerBoundary 0.0
>>> upperBoundary 30.0
>>>
>>> upperWallConstant 100.0
>>>
>>> distanceZ {
>>> forceNoPBC yes
>>> main {
>>> atomsFile labels.pdb
>>> atomsCol B
>>> atomsColValue 1.0
>>> }
>>> ref {
>>> atomsFile labels.pdb
>>> atomsCol B
>>> atomsColValue 2.0
>>> }
>>> }
>>> }
>>>
>>> colvar {
>>>
>>> name d2
>>>
>>> outputAppliedForce on
>>> width 1
>>>
>>> lowerBoundary 0.0
>>> upperBoundary 10.0
>>>
>>> upperWallConstant 100.0
>>>
>>> coordNum {
>>> cutoff 4.0
>>>
>>>
>>> group1 {
>>> atomsFile labels.pdb
>>> atomsCol O
>>> atomsColValue 1.0
>>> }
>>> group2 {
>>> atomsFile labels.pdb
>>> atomsCol B
>>> atomsColValue 2.0
>>> }
>>> }
>>> }
>>>
>>>
>>>
>>>
>>>
>>> metadynamics {
>>> colvars d1 d2
>>>
>>> useGrids on
>>> hillWeight 0.01
>>> newHillFrequency 100
>>> dumpFreeEnergyFile on
>>> dumpPartialFreeEnergyFile on
>>> saveFreeEnergyFile on
>>> writeHillsTrajectory on
>>>
>>> multipleReplicas yes
>>> replicaID rep1
>>> replicasRegistry replicas.registry.txt
>>> replicaUpdateFrequency 1000
>>> }
>>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Research collaborator, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
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