[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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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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