[gmx-users] Re: gmx-users Digest, Vol 83, Issue 217

Raghuvir R S Pissurlenkar raghuvir at bcpindia.org
Thu Mar 31 08:52:54 CEST 2011


Thanks Justin

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Sent: Thursday, March 31, 2011 11:49 AM
Subject: gmx-users Digest, Vol 83, Issue 217


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> Today's Topics:
>
>   1. Heat of vap (Elisabeth)
>   2. Re: Heat of vap (David van der Spoel)
>   3. Re: Heat of vap (Justin A. Lemkul)
>   4. Help on umbrella sampling (raghuvir at bcpindia.org)
>   5. Re: Help on umbrella sampling (Justin A. Lemkul)
>   6. the total charge of system is not an integer (ahmet y?ld?r?m)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 30 Mar 2011 15:22:56 -0400
> From: Elisabeth <katesedate at gmail.com>
> Subject: [gmx-users] Heat of vap
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTin4-pgXw2NtOhsqn3Gpxfzu+ZXpQvY4yJ5YXPyV at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear all,
>
> I intend to obtain vaporization heat per volume for a *pure alkane 
> system*.
> Here is the steps I am taking. Please correct me.
>
> 1- Obtain total energy of system (kinetic+potential) and divide by number 
> of
> molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol 
> XXX
> 2- Obtain total energy of a single molecule (use pbc).
> 3- Subtract step 2 from step 1.
> 4- Divide by simulation box volume.
>
> My questions is:
>
> in step 2 : what should be the box size? The same size as in 1 or it does
> not matter? (step 1 is done for the actual denstiy)
>
> Thanking you all,
> Regards,
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>
> Message: 2
> Date: Wed, 30 Mar 2011 21:31:22 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Heat of vap
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D93850A.3020202 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 2011-03-30 21.22, Elisabeth wrote:
>> Dear all,
>>
>> I intend to obtain vaporization heat per volume for a /pure alkane
>> system/.  Here is the steps I am taking. Please correct me.
>>
>> 1- Obtain total energy of system (kinetic+potential) and divide by
>> number of molecules to obtain energy per mol of molecules. g_energy -f
>> *.edr -nmol XXX
>> 2- Obtain total energy of a single molecule (use pbc).
>> 3- Subtract step 2 from step 1.
>> 4- Divide by simulation box volume.
>>
>> My questions is:
>>
>> in step 2 : what should be the box size? The same size as in 1 or it
>> does not matter? (step 1 is done for the actual denstiy)
> do turn off all pbc and cutoff for that one.
>>
>> Thanking you all,
>> Regards,
>>
>
>
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 30 Mar 2011 15:30:12 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Heat of vap
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D9384C4.2040504 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Elisabeth wrote:
>> Dear all,
>>
>> I intend to obtain vaporization heat per volume for a /pure alkane
>> system/.  Here is the steps I am taking. Please correct me.
>>
>> 1- Obtain total energy of system (kinetic+potential) and divide by
>> number of molecules to obtain energy per mol of molecules. g_energy -f
>> *.edr -nmol XXX
>> 2- Obtain total energy of a single molecule (use pbc).
>> 3- Subtract step 2 from step 1.
>> 4- Divide by simulation box volume.
>>
>> My questions is:
>>
>> in step 2 : what should be the box size? The same size as in 1 or it
>> does not matter? (step 1 is done for the actual denstiy)
>>
>
> More troubling, how does one define the energy of a molecule?  If you use 
> any
> sort of long-range algorithms (especially PME, but also dispersion 
> correction),
> you can't simply decompose the system like this.
>
> In the derivation of recent Gromos96 parameter sets, the heat of 
> vaporization is
> quite simple:
>
> DHvap = <Ugas> - <Uliq> + RT
>
> I have seen this equation used in a number of other studies, as well.
>
> -Justin
>
>> Thanking you all,
>> Regards,
>>
>
> -- 
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 31 Mar 2011 02:14:50 +0530
> From: raghuvir at bcpindia.org
> Subject: [gmx-users] Help on umbrella sampling
> To: gmx-users at gromacs.org
> Message-ID: <20110331021450.tr893fal8cg8ks0c at www.bcpindia.org>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> Dear Users and Developers
>
> I am trying to execute md_pull.mdp {given below} on a small molecule
> embedded at the core of lipid bilayer.  I have tried to modify the
> md_pull.mdp from the Tutorial by Justin Lemkul on Umbrella sampling.
> I encounter LINCS warning  (1000) after about 100-110 ps of the
> simulation resulting in termination of mdrun. This occurs when the
> small molecule is near the polar heads.  I understand the system is
> exploding.
>
> I have minimized the system, followed by anneal to 323K then nvt and
> npt after which I perform the md_pull.  How can I soften the core {as
> mentioned in the errors on www.gromacs.org} or any other alternative
> is there adding lincs warning to mdp file {I am not aware}
>
> Following is the md_pull.mdp file as modified;
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> title = Umbrella pulling simulation
> define = -DPOSRES_DPPC
> ; Run parameters
> integrator = md
> dt = 0.002
> tinit = 0
> nsteps = 100000 ; 200 ps
> nstcomm = 1
> ; Output parameters
> nstxout = 5000 ; every 10 ps
> nstvout = 5000
> nstfout = 500
> nstxtcout = 500 ; every 1 ps
> nstenergy = 500
> ; Bond parameters
> constraint_algorithm = lincs
> constraints = all-bonds
> continuation = yes ; continuing from NPT
> ; Single-range cutoff scheme
> nstlist = 5
> ns_type = grid
> rlist = 1.4
> rcoulomb = 1.4
> rvdw = 1.4
> ; PME electrostatics parameters
> coulombtype = PME
> fourierspacing  = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = Nose-Hoover
> tc_grps = TPF DPPC SOL
> tau_t = 0.1 0.1 0.1
> ref_t = 323 323 323
> ; Pressure coupling is on
> pcoupl = Parrinello-Rahman     ; Pressure coupling on in NPT
> pcoupltype = semiisotropic     ; uniform scaling of x-y box vectors,
> independent z
> tau_p = 2.0         ; time constant, in ps
> ref_p = 1.0 1.0         ; reference pressure, x-y, z (in bar)
> compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1
> ; Generate velocities is off
> gen_vel = no
> ; Periodic boundary conditions are on in all directions
> pbc = xyz
> ; Long-range dispersion correction
> DispCorr = EnerPres
> ; Pull code
> pull = umbrella
> pull_geometry = distance
> pull_dim = N N Y
> pull_start = yes ; define initial COM distance > 0
> pull_ngroups = 1
> pull_group0 = DPPC
> pull_group1 = TPF
> pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns
> pull_k1 = 1000 ; kJ mol^-1 nm^-2
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Please help me
>
> Thanks N Regards
>
> Raghuvir
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 30 Mar 2011 17:54:02 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Help on umbrella sampling
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D93A67A.9010005 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> raghuvir at bcpindia.org wrote:
>> Dear Users and Developers
>>
>> I am trying to execute md_pull.mdp {given below} on a small molecule
>> embedded at the core of lipid bilayer.  I have tried to modify the
>> md_pull.mdp from the Tutorial by Justin Lemkul on Umbrella sampling.  I
>> encounter LINCS warning  (1000) after about 100-110 ps of the simulation
>> resulting in termination of mdrun. This occurs when the small molecule
>> is near the polar heads.  I understand the system is exploding.
>>
>> I have minimized the system, followed by anneal to 323K then nvt and npt
>> after which I perform the md_pull.  How can I soften the core {as
>> mentioned in the errors on www.gromacs.org} or any other alternative is
>> there adding lincs warning to mdp file {I am not aware}
>>
>
> "Soft core" is a mechanism by which Lennard-Jones interactions are 
> modified
> while doing decoupling/annihilation calculations.  This point is not 
> relevant here.
>
> I see that you're restraining the lipids in some way.  Which atoms are
> restrained?  In which directions?  Why are you restraining them?  I would 
> assume
> that as a molecule is pulled through your membrane, any artificial forces 
> that
> work against one another would cause instability.
>
> -Justin
>
>> Following is the md_pull.mdp file as modified;
>> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
>> title        = Umbrella pulling simulation
>> define        = -DPOSRES_DPPC
>> ; Run parameters
>> integrator    = md
>> dt        = 0.002
>> tinit        = 0
>> nsteps        = 100000    ; 200 ps
>> nstcomm        = 1
>> ; Output parameters
>> nstxout        = 5000        ; every 10 ps
>> nstvout        = 5000
>> nstfout        = 500
>> nstxtcout    = 500        ; every 1 ps
>> nstenergy    = 500
>> ; Bond parameters
>> constraint_algorithm     = lincs
>> constraints        = all-bonds
>> continuation         = yes        ; continuing from NPT
>> ; Single-range cutoff scheme
>> nstlist        = 5
>> ns_type        = grid
>> rlist        = 1.4
>> rcoulomb    = 1.4
>> rvdw        = 1.4
>> ; PME electrostatics parameters
>> coulombtype    = PME
>> fourierspacing  = 0.12
>> fourier_nx    = 0
>> fourier_ny     = 0
>> fourier_nz    = 0
>> pme_order    = 4
>> ewald_rtol    = 1e-5
>> optimize_fft    = yes
>> ; Berendsen temperature coupling is on in two groups
>> Tcoupl         =    Nose-Hoover
>> tc_grps    =    TPF    DPPC    SOL
>> tau_t    =    0.1    0.1    0.1
>> ref_t    =    323    323    323
>> ; Pressure coupling is on
>> pcoupl        = Parrinello-Rahman        ; Pressure coupling on in NPT
>> pcoupltype    = semiisotropic            ; uniform scaling of x-y box
>> vectors, independent z
>> tau_p        = 2.0                    ; time constant, in ps
>> ref_p        = 1.0    1.0                ; reference pressure, x-y, z
>> (in bar)
>> compressibility = 4.5e-5    4.5e-5    ; isothermal compressibility, 
>> bar^-1
>> ; Generate velocities is off
>> gen_vel        = no
>> ; Periodic boundary conditions are on in all directions
>> pbc        = xyz
>> ; Long-range dispersion correction
>> DispCorr    = EnerPres
>> ; Pull code
>> pull        = umbrella
>> pull_geometry    = distance
>> pull_dim    = N N Y
>> pull_start    = yes        ; define initial COM distance > 0
>> pull_ngroups    = 1
>> pull_group0    = DPPC
>> pull_group1    = TPF
>> pull_rate1    = 0.01        ; 0.01 nm per ps = 10 nm per ns
>> pull_k1        = 1000        ; kJ mol^-1 nm^-2
>> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
>> Please help me
>>
>> Thanks N Regards
>>
>> Raghuvir
>>
>
> -- 
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 31 Mar 2011 09:18:31 +0300
> From: ahmet y?ld?r?m <ahmedo047 at gmail.com>
> Subject: [gmx-users] the total charge of system is not an integer
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTinPb72XRj2Fd1snOjAqu3jS9MLy8DT3LBLVA0us at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear users,
>
> Before energy minimization step , I performed the preprosessing step using
> grompp .
> However, there are two note that :
>
> *NOTE 1 [file topol.top, line 52]:*
>  System has non-zero total charge: -1.500000e+01
>
> *NOTE 2 [file topol.top]:*
>  The largest charge group contains 11 atoms.
>  Since atoms only see each other when the centers of geometry of the 
> charge
>  groups they belong to are within the cut-off distance, too large charge
>  groups can lead to serious cut-off artifacts.
>  For efficiency and accuracy, charge group should consist of a few atoms.
>  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
> *
> PS: *TRS and EDO are not aminoacid*
>
> TRS.itp:*
> ..
> [ moleculetype ]
> ; Name nrexcl
> TRS      3
>
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>     1        OA     1  TRS      O1     1   -0.119  15.9994
>     2         H     1  TRS     H13     1    0.032   1.0080
>     3       CH2     1  TRS      C1     1    0.087  14.0270
>     4      CCl4     1  TRS       C     2    0.055  12.0110
>     5       CH2     1  TRS      C3     2    0.049  14.0270
>     6        OA     1  TRS      O3     2   -0.205  15.9994
>     7         H     1  TRS     H33     2    0.019   1.0080
>     8        NL     1  TRS       N     2    0.206  14.0067
>     9         H     1  TRS      H2     2    0.004   1.0080
>    10         H     1  TRS      H3     2    0.004   1.0080
>    11         H     1  TRS      H1     2    0.004   1.0080
>    12       CH2     1  TRS      C2     2    0.050  14.0270
>    13        OA     1  TRS      O2     2   -0.205  15.9994
>    14         H     1  TRS     H23     2    0.019   1.0080
> ...
>
> *EDO.itp*
> ...
> [ moleculetype ]
> ; Name nrexcl
> EDO      3
>
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>     1        OA     1  EDO     OAB     1   -0.111  15.9994
>     2         H     1  EDO     HAE     1    0.031   1.0080
>     3       CH2     1  EDO     CAA     1    0.080  14.0270
>     4       CH2     1  EDO     CAC     1    0.080  14.0270
>     5        OA     1  EDO     OAD     1   -0.111  15.9994
>     6         H     1  EDO     HAF     1    0.031   1.0080
> ...
> *
> topol.top:*
> ..
> ; Include water topology
> #include "gromos43a1.ff/spc.itp"
> #include "TRS.itp"
> #include "EDO.itp"
> ..
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Protein_chain_B     1
> SOL               185
> SOL               143
> TRS                1
> EDO                1
> SOL             44125
> *
> Conf.gro:*
> MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
> 5354
>    2GLN      N    1   1.458  -1.158   0.739
>    2GLN     H1    2   1.520  -1.083   0.763
> .......
>  485HOH    HW1 5333   0.221  -3.864  -2.291
>  485HOH    HW2 5334   0.303  -3.946  -2.407
>    1TRS  O1       1  -3.812  -0.471  -2.002
>    1TRS  H13      2  -3.865  -0.443  -1.922
>    1TRS  C1       3  -3.672  -0.469  -1.971
>    1TRS  C        4  -3.635  -0.571  -1.863
>    1TRS  C3       5  -3.711  -0.547  -1.731
>    1TRS  O3       6  -3.694  -0.414  -1.679
>    1TRS  H33      7  -3.746  -0.404  -1.594
>    1TRS  N        8  -3.673  -0.705  -1.911
>    1TRS  H2       9  -3.625  -0.725  -1.996
>    1TRS  H3      10  -3.771  -0.707  -1.927
>    1TRS  H1      11  -3.649  -0.774  -1.842
>    1TRS  C2      12  -3.483  -0.573  -1.840
>    1TRS  O2      13  -3.428  -0.445  -1.806
>    1TRS  H23     14  -3.470  -0.412  -1.722
>    1EDO  OAB      1   0.307  -2.792   0.149
>    1EDO  HAE      2   0.390  -2.826   0.104
>    1EDO  CAA      3   0.239  -2.901   0.212
>    1EDO  CAC      4   0.111  -2.851   0.281
>    1EDO  OAD      5   0.144  -2.763   0.388
>    1EDO  HAF      6   0.060  -2.731   0.432
>   8.13100   7.04165  13.54850   0.00000   0.00000  -4.06550   0.00000
> 0.00000   0.00000
>
> How can I fixed these notes(note 1 and note 2)?
>
> Thanks in advance
> -- 
> Ahmet YILDIRIM
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