From: Jessen Lucas (jessenlucas0_at_gmail.com)
Date: Tue Feb 07 2017 - 10:58:22 CST
Dear Jerome,
The error appeared, even after I changed the RMSDs' lower boundary to
0.5, ERROR: Atom 14 velocity is 5.81379e+13 -2.90689e+13 -2.065 (limit is
22000, atom 13 of 54 on patch 1 pe 8)
I use the pdb and psf files from ABF tutorial together with your helix,
310turn, omega files, I guess it should be work. I have no idea about why
it did not work. (I run one dimension sucessfully, the distance colvar).
Best,
Lucas
2017-02-08 0:43 GMT+08:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:
> Dear Lucas,
>
> Did the simulation run at all? There is a large singularity around RMSD=0,
> so you cannot start the simulation from one of the reference states, it
> will blow up. Actually the safest is to exclude the region of very low RMSD
> from the ABF calculation (maybe below 0.2 A or something).
>
> Jerome
>
>
>
>
> On 7 February 2017 at 16:28, Jessen Lucas <jessenlucas0_at_gmail.com> wrote:
>
>> Dear Jerome,
>>
>>
>> I am sorry to disturb you again, I tried to use ABF in NAMD to run
>> deca-alanine in your paper using three RMSD collective variables, however
>> it did not work, the .grad file show me all 0. Could you help me to point
>> out the problem, or may I have your files about this case?
>>
>> The following is my namd conf file and colvar in file
>>
>> # NUMBER OF MD-STEPS
>>
>> numsteps 5000000
>>
>>
>> # TOPOLOGY
>>
>> structure deca-ala.psf
>>
>>
>> # FORCE FIELD
>>
>> parameters par_all22_prot.inp
>> paraTypeCharmm on
>>
>>
>> # 1-4 TERMs
>>
>> exclude scaled1-4
>> 1-4scaling 1.0
>>
>>
>> # INPUT FILES
>>
>> coordinates deca-ala.pdb
>>
>> temperature 300.0
>>
>>
>> # OUTPUT FILES
>>
>> binaryoutput no
>> binaryrestart yes
>>
>> outputname abf_00_0
>> restartname abf_00
>>
>>
>> # DCD FILE
>>
>> dcdFile abf_00.dcd
>>
>>
>> # FREQUENCY FOR DUMPING OUTPUT DATA
>>
>> outputenergies 1000
>> outputtiming 1000
>> outputpressure 1000
>> restartfreq 1000
>> XSTFreq 1000
>> dcdFreq 1000
>>
>>
>> # CUT-OFFs
>>
>> hgroupcutoff 2.8
>> switching on
>> switchdist 9.0
>> cutoff 11.0
>> pairlistdist 12.0
>>
>>
>> # CONSTANT-T
>>
>> langevin on
>> langevintemp 300.0
>> langevindamping 10.0
>>
>>
>> # MULTIPLE TIME-STEP PROPAGATOR
>>
>> timestep 0.5
>>
>>
>> # SHAKE/RATTLE
>>
>> rigidbonds none
>>
>>
>> # PARALLELISM
>>
>> stepspercycle 20
>> splitpatch hydrogen
>> margin 1.0
>>
>>
>> # ABF SECTION
>>
>> colvars on
>> colvarsConfig Distance.in
>> ##################################################
>>
>> colvarsTrajFrequency 500
>> colvarsRestartFrequency 500
>>
>>
>> colvar {
>> name rmsdA
>>
>> outputTotalForce on
>> # outputAppliedForce on
>> width 1.0
>>
>> lowerBoundary 0.0
>> upperBoundary 5.0
>>
>> lowerWallConstant 100.0
>> upperWallConstant 100.0
>>
>> rmsd {
>> atoms {
>> atomNumbers 4 14 24 34 44 54 64 74 84 99
>> }
>> refpositionsfile helix.pdb
>> }
>> }
>>
>>
>> colvar {
>> name rmsdB
>>
>> outputTotalForce on
>> # outputAppliedForce on
>> width 1.0
>>
>> lowerBoundary 0.0
>> upperBoundary 5.0
>>
>> lowerWallConstant 100.0
>> upperWallConstant 100.0
>>
>> rmsd {
>> atoms {
>> atomNumbers 10 20 30 40 50 60 70 80 90 92
>> }
>> refpositionsfile 310turn.pdb
>> }
>> }
>>
>>
>> colvar {
>> name rmsdC
>>
>> outputTotalForce on
>> # outputAppliedForce on
>> width 1.0
>>
>> lowerBoundary 0.0
>> upperBoundary 5.0
>>
>> lowerWallConstant 100.0
>> upperWallConstant 100.0
>>
>> rmsd {
>> atoms {
>> atomNumbers 12 22 32 42 52 62 72 82 97
>> }
>> refpositionsfile omega.pdb
>> }
>> }
>>
>>
>> abf {
>> colvars rmsdA rmsdB rmsdC
>> fullSamples 100
>> }
>>
>>
>> Is there something wrong in this files? I just follow the tutorial.
>>
>> Best regards,
>> Lucas
>>
>>
>> 2017-02-01 21:58 GMT+08:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:
>>
>>> Yes, it is written for arbitrary dimension.
>>>
>>> Jerome
>>>
>>> On 1 February 2017 at 14:40, Jessen Lucas <jessenlucas0_at_gmail.com>
>>> wrote:
>>>
>>>> Thank you, so the abf_integrate works for high dimension?
>>>>
>>>> Lucas
>>>>
>>>> 2017-02-01 21:20 GMT+08:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:
>>>>
>>>>> Yes, except that you dont want those lines!
>>>>> centerReference no
>>>>> rotateReference no
>>>>>
>>>>> Once you have integrated the free energy gradient with abf_integrate,
>>>>> you get the PMF in a plain text file. You can plot it, but you can also
>>>>> open it in a text editor, and you'll find individual values in there.
>>>>>
>>>>> Jerome
>>>>>
>>>>>
>>>>> On 1 February 2017 at 14:16, Jessen Lucas <jessenlucas0_at_gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Thanks Jerome, so it should be like the following?
>>>>>>
>>>>>> colvar {
>>>>>> name rmsdA
>>>>>>
>>>>>> width 1.0
>>>>>>
>>>>>> lowerBoundary 0.0
>>>>>> upperBoundary 5.0
>>>>>>
>>>>>> lowerWallConstant 100.0
>>>>>> upperWallConstant 100.0
>>>>>>
>>>>>> rmsd {
>>>>>> atoms {
>>>>>> atomNumbersRange 1-104
>>>>>> centerReference no
>>>>>> rotateReference no
>>>>>> }
>>>>>> refpositionsfile ../Common/omega-ideal.pdb
>>>>>> }
>>>>>> }
>>>>>>
>>>>>> And I saw the ABF output the whole free energy landscape, is there
>>>>>> anyway to get one point free energy? for example, the free energy value at
>>>>>> rmsdA=3, rmsdB=4?
>>>>>>
>>>>>> Thank you very much for your kindly reply.
>>>>>> Lucas
>>>>>>
>>>>>> 2017-02-01 21:07 GMT+08:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:
>>>>>>
>>>>>>> Your syntax for the RMSD components is not correct. The "atoms"
>>>>>>> block needs to contain the definition of which atoms are involved. The
>>>>>>> "refpositionsfile" is a parameter of the rmsd function, so it should be
>>>>>>> outside that block.
>>>>>>>
>>>>>>> Best,
>>>>>>> Jerome
>>>>>>>
>>>>>>> On 31 January 2017 at 17:04, Jessen Lucas <jessenlucas0_at_gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Dear Jerome,
>>>>>>>>
>>>>>>>> I found that in github colvars
>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_colvars_colvars&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=i83dq7tEuia45zFsvze217Dl3QR4ygres_qi16tY7xU&s=BPqNf54jff0GZnsV9qDB5_TyL-vmmzxJCxGv7DXMzzA&e=>
>>>>>>>> /namd
>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_colvars_colvars_tree_master_namd&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=i83dq7tEuia45zFsvze217Dl3QR4ygres_qi16tY7xU&s=z9SA_KG80pGsEuFAgT1_Wh_l3U_Bln-cHm8FGtvNHU4&e=>
>>>>>>>> /tests
>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_colvars_colvars_tree_master_namd_tests&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=i83dq7tEuia45zFsvze217Dl3QR4ygres_qi16tY7xU&s=VRHQSpFoobNIjYT4dF6jkIJxsyLxy3cJqTTlKI_eazg&e=>
>>>>>>>> /library
>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_colvars_colvars_tree_master_namd_tests_library&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=i83dq7tEuia45zFsvze217Dl3QR4ygres_qi16tY7xU&s=dN7xFNniZSYnuJj9_W8kpjcJsnxM-ulZ5pOI6r-yTk4&e=>
>>>>>>>> /001_10ala_RMSD
>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_colvars_colvars_tree_master_namd_tests_library_001-5F10ala-5FRMSD&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=i83dq7tEuia45zFsvze217Dl3QR4ygres_qi16tY7xU&s=_vxHuW7Gq0XDMSTpKyG2GUzlQCaNaHVHl9lyaKBbyko&e=>
>>>>>>>> /, you use 5 rmsd as collective variables. However when I tried to
>>>>>>>> change those collective variables to the three rmsd collective variables as
>>>>>>>> in your paper "Exploring Multidimensional Free Energy Landscapes
>>>>>>>> Using Time-Dependent Biases on Collective Variables"?
>>>>>>>>
>>>>>>>> Is the following colvar config correct?
>>>>>>>>
>>>>>>>> colvar {
>>>>>>>> name rmsdA
>>>>>>>>
>>>>>>>> outputTotalForce on
>>>>>>>>
>>>>>>>> width 1.0
>>>>>>>>
>>>>>>>> lowerBoundary 0.0
>>>>>>>> upperBoundary 5.0
>>>>>>>>
>>>>>>>> lowerWallConstant 100.0
>>>>>>>> upperWallConstant 100.0
>>>>>>>>
>>>>>>>> rmsd {
>>>>>>>> atoms {
>>>>>>>> refpositionsfile ../Common/310turn-ideal.pdb
>>>>>>>> }
>>>>>>>> }
>>>>>>>> }
>>>>>>>>
>>>>>>>> colvar {
>>>>>>>> name rmsdB
>>>>>>>>
>>>>>>>> outputTotalForce on
>>>>>>>>
>>>>>>>> width 1.0
>>>>>>>>
>>>>>>>> lowerBoundary 0.0
>>>>>>>> upperBoundary 5.0
>>>>>>>>
>>>>>>>> lowerWallConstant 100.0
>>>>>>>> upperWallConstant 100.0
>>>>>>>>
>>>>>>>> rmsd {
>>>>>>>> atoms {
>>>>>>>> refpositionsfile ../Common/helix-ideal.pdb
>>>>>>>> }
>>>>>>>> }
>>>>>>>> }
>>>>>>>>
>>>>>>>> colvar {
>>>>>>>> name rmsdC
>>>>>>>>
>>>>>>>> outputTotalForce on
>>>>>>>>
>>>>>>>> width 1.0
>>>>>>>>
>>>>>>>> lowerBoundary 0.0
>>>>>>>> upperBoundary 5.0
>>>>>>>>
>>>>>>>> lowerWallConstant 100.0
>>>>>>>> upperWallConstant 100.0
>>>>>>>>
>>>>>>>> rmsd {
>>>>>>>> atoms {
>>>>>>>> refpositionsfile ../Common/omega-ideal.pdb
>>>>>>>> }
>>>>>>>> }
>>>>>>>> }
>>>>>>>>
>>>>>>>> I do not why it did not work when I do a small change? After that
>>>>>>>> instead of using colvar module of NAMD, I use tcl script I could calculate
>>>>>>>> the rmsd, but I do not know how to calculate the free energy at the point.
>>>>>>>>
>>>>>>>> Could you give me a suggestion?
>>>>>>>> Thanks in advance.
>>>>>>>>
>>>>>>>> Lucas
>>>>>>>>
>>>>>>>>
>>>>>>>> 2017-01-14 7:48 GMT+08:00 Jessen Lucas <jessenlucas0_at_gmail.com>:
>>>>>>>>
>>>>>>>>> Thank you, dear Jerome. :)
>>>>>>>>>
>>>>>>>>> 2017-01-14 0:31 GMT+08:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:
>>>>>>>>>
>>>>>>>>>> Dear Lucas,
>>>>>>>>>>
>>>>>>>>>> Here are the files in question.
>>>>>>>>>>
>>>>>>>>>> Jerome
>>>>>>>>>>
>>>>>>>>>> On 13 January 2017 at 15:55, Jessen Lucas <jessenlucas0_at_gmail.com
>>>>>>>>>> > wrote:
>>>>>>>>>>
>>>>>>>>>>> Dear Jerome,
>>>>>>>>>>>
>>>>>>>>>>> Yes, I want to use the same system, may I have your files these
>>>>>>>>>>> three conformations, since I want to get the same result as yours,
>>>>>>>>>>> otherwise it is hard to convince myself. Thanks a lot.
>>>>>>>>>>>
>>>>>>>>>>> Best regards,
>>>>>>>>>>> Lucas
>>>>>>>>>>>
>>>>>>>>>>> 2017-01-13 16:57 GMT+08:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Lucas,
>>>>>>>>>>>>
>>>>>>>>>>>> For that work, the reference conformations were not strictly
>>>>>>>>>>>> speaking "ideal" (if I wrote that, it was a poor choice of words). They
>>>>>>>>>>>> were local energy minima of that particular peptide under those particular
>>>>>>>>>>>> conditions, and I selected them from ABF trajectories using different
>>>>>>>>>>>> coordinates.
>>>>>>>>>>>>
>>>>>>>>>>>> If you are simulating the very same system, I will gladly share
>>>>>>>>>>>> the files I used (perhaps off-list) - however they don't have any general
>>>>>>>>>>>> value: some of them are rather idiosyncratic of that peptide.
>>>>>>>>>>>>
>>>>>>>>>>>> Best,
>>>>>>>>>>>> Jerome
>>>>>>>>>>>>
>>>>>>>>>>>> On 13 January 2017 at 03:09, Jessen Lucas <
>>>>>>>>>>>> jessenlucas0_at_gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Dear all,
>>>>>>>>>>>>>
>>>>>>>>>>>>> I am reading "Exploring Multidimensional Free Energy
>>>>>>>>>>>>> Landscapes Using Time-Dependent Biases on Collective Variables", in there,
>>>>>>>>>>>>> I want to plot the free energy landscape, I saw there use three collective
>>>>>>>>>>>>> variables, the rmsd with respective to the ideal
>>>>>>>>>>>>> alpha-helical, ω-shaped γ-turn, and turn/310-helix conformations,
>>>>>>>>>>>>> respectively. My question is how to set this three collective variables in
>>>>>>>>>>>>> NAMD? I do not know what the conformations of ideal
>>>>>>>>>>>>> alpha-helical, ω-shaped γ-turn, and turn/310-helix.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks for any kindly suggestion.
>>>>>>>>>>>>> Lucas
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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