[gmx-users] Problem fpr building a peptide with two modified residues with amber ff
Justin Lemkul
jalemkul at vt.edu
Sun Jan 14 23:36:39 CET 2018
On 1/14/18 12:04 PM, ABEL Stephane wrote:
> Thank you, Justin for your interest to my problem,
>
> But even if I use the -missing argument*, pdb2gmx still wants to add an Nter ILE instead of a central a simple ILE :((
Ile should not be treated as a terminal residue, and it wasn't in the
screen output you provided before after adding your custom residues to
residuetypes.dat. That's a prerequisite if you want anything to work.
Getting the connectivity right after dealing with the custom residues is
the next problem after that.
-Justin
> *gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o Atosiban_amber14sb.pdb -i Atosiban_posre.itp -missing
>
> I will try to search a workaround
>
> Best
>
> Stéphane
>
> ________________________________________
> De : ABEL Stephane
> Envoy? : dimanche 14 janvier 2018 16:52
> ? : gromacs.org_gmx-users at maillist.sys.kth.se
> Objet : RE:gromacs.org_gmx-users Digest, Vol 165, Issue 50
>
> Thanks Justin
>
> First I forgot to say that I am building a cyclic peptide (Atosiban, https://fr.wikipedia.org/wiki/Atosiban). I construct two RTP for the MER (3-Mercaptopropionyl-) and TYO (ethoxy tyrosine. And they are correct since the two residues are well constructed and linked together with pdb2gmx as it is shown If I consider the ILE as NILE
>
> For linking the MER and CYX I define a bond with the specbond.dat (the corresponding bond is shown in the pdb2gmx output). The only problem I have is that NILE residue is chosen instead of ILE
>
> How to resolve this problem and to force pdb2gmx to use ILE ? It is strange or I found a subtle error I cannot find.
>
> St?phane
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 14 Jan 2018 10:34:08 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Problem fpr building a peptide with two
> modified residues with amber ff
> Message-ID: <541ddbd0-378e-16eb-79a4-f161235d4d22 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 1/14/18 10:04 AM, ABEL Stephane wrote:
>> Hi Justin
>>
>> I have added the TYO and MER residue as Protein is the residuetypes.dat. And the the following output with pdb2gmx. I select 2 and 6
>>
>> ##########
>> gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes
>>
>>
>> Select the Force Field:
>> From '/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top/':
>> 1: Amber12sb ff99SB + new backbone and side chain torsion for protein
>> 2: AMBER14SB_parmbsc1 (ff14SB for protein + parmbsc1 for DNA)
>> 3: AMBER94 BCL force field (J. Comp. Chem. 2012, 33, 1969?1980)
>> 4: CHARMM36 all-atom force field (July 2017)
>> 5: CHARMM36 all-atom force field, surfactants and pigments
>> 6: GLYCAM06 force field for alkylglycosides and RG1 (2011, J. Phys. Chem. B 2011, 115, 487-499 )
>> 7: GROMOS96 2016H66 force field (J. Chem. Theory. Comput., 2016, 12, 3825?3850)
>> 8: GROMOS96 53a6 force field with PVP (JCC 2004 vol 25 pag 1656 and J. Phys. Chem. C, 2015, 119 (14), pp 7888?7899)
>> 9: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 10.1002/jcc.21675)
>> 10: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
>> From '/ccc/products/gromacs-5.1.2/default/share/gromacs/top':
>> 11: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
>> 12: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
>> 13: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
>> 14: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
>> 15: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
>> 16: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
>> 17: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
>> 18: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
>> 19: GROMOS96 43a1 force field
>> 20: GROMOS96 43a2 force field (improved alkane dihedrals)
>> 21: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>> 22: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>> 23: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>> 24: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
>> 25: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>> 2
>>
>> Using the Amber14sb_parmbsc1 force field in directory /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff
>>
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/watermodels.dat
>>
>> Select the Water Model:
>> 1: TIP3P TIP 3-point, recommended
>> 2: TIP4P TIP 4-point
>> 3: TIP4P-Ew TIP 4-point optimized with Ewald
>> 4: SPC simple point charge
>> 5: SPC/E extended simple point charge
>> 6: None
>> 6
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.r2b
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.r2b
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.r2b
>> Reading Atosiban_box_ctr.pdb...
>> Read 'GROningen MAchine for Chemical Simulation', 85 atoms
>> Analyzing pdb file
>> Splitting chemical chains based on TER records or chain id changing.
>> There are 1 chains and 0 blocks of water and 10 residues with 85 atoms
>>
>> chain #res #atoms
>> 1 'A' 10 85
>>
>> All occupancies are one
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/atomtypes.atp
>> Atomtype 89Reading residue database... (amber14sb_parmbsc1)
>>
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/Merca.rtp
>> Residue 1
>> Sorting it all out...
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/TYO.rtp
>> Residue 2
>> Sorting it all out...
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.rtp
>> Residue 95
>> Sorting it all out...
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.rtp
>> Residue 111
>> Sorting it all out...
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.rtp
>> Residue 127
>> Sorting it all out...
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.hdb
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.hdb
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.hdb
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.n.tdb
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.c.tdb
>>
>> Back Off! I just backed up Atosiban_amber14sb.top to ./#Atosiban_amber14sb.top.6#
>> Processing chain 1 'A' (85 atoms, 10 residues)
>> Identified residue MER1 as a starting terminus.
>> Identified residue NH210 as a ending terminus.
>> 1 out of 1 lines of specbond.dat converted successfully
>> Special Atom Distance matrix:
>> MER1
>> S11
>> CYX6 SG63 0.200
>> Linking MER-1 S1-1 and CYX-6 SG-63...
>>
>> -------------------------------------------------------
>> Program gmx pdb2gmx, VERSION 5.1.2
>> Source code file: /tmp/gromacs/5.1.2/iomkl-156233.188/gromacs-5.1.2/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1083
>>
>> Fatal error:
>> There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Fix your terminal residues so that they match the residue database (.rtp) entries, or provide terminal database entries (.tdb).
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>> ####
>>
>> Now indeed the MER and TYO as recognized as residues but I still obtain the dangling bond error
> The AMBER force fields are unique in that they do not support terminal
> group patching; your residue definitions for any terminal residues must
> be complete. I suspect your N-terminal MER residue does not have the
> proper -NH3+ terminus already built, so when pdb2gmx checks, it finds
> missing atoms. You need to specifically parametrize this residue in its
> terminal, not internal, form and supply that as your .rtp entry.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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> End of gromacs.org_gmx-users Digest, Vol 165, Issue 50
> ******************************************************
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 14 Jan 2018 10:55:19 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue
> 50
> Message-ID: <d44769fa-da75-16f2-fbae-4ff815bb13c0 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 1/14/18 10:52 AM, ABEL Stephane wrote:
>> Thanks Justin
>>
>> First I forgot to say that I am building a cyclic peptide (Atosiban, https://fr.wikipedia.org/wiki/Atosiban). I construct two RTP for the MER (3-Mercaptopropionyl-) and TYO (ethoxy tyrosine. And they are correct since the two residues are well constructed and linked together with pdb2gmx as it is shown If I consider the ILE as NILE
>>
>> For linking the MER and CYX I define a bond with the specbond.dat (the corresponding bond is shown in the pdb2gmx output). The only problem I have is that NILE residue is chosen instead of ILE
>>
>> How to resolve this problem and to force pdb2gmx to use ILE ? It is strange or I found a subtle error I cannot find.
> I've never dealt with cyclic peptides in GROMACS and most threads about
> them tend to die off without resolution. It's not something pdb2gmx does
> well. Presumably you could use the -missing flat (very dangerous!) and
> then verify that the topology has all the special bonds it needs.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 14 Jan 2018 17:29:35 +0100
> From: Faezeh Pousaneh <fpoosaneh at gmail.com>
> To: gmx-users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] rlist
> Message-ID:
> <CAJtnTaXQrZF-YT28ugfs=Mni+TpVg0TbeZH=f3DjytmqBt7iwg at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thank you Justin, now I understood. However, I do not have any target data
> for my system. What do you suggest? the longer rcoulomb is safer, right?
>
>
> Best regards
>
>
> On Sun, Jan 14, 2018 at 4:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 1/14/18 10:42 AM, Faezeh Pousaneh wrote:
>>
>>> Thanks Justin. But I only define vdW potential form, coulomb potential
>>> form
>>> is as in Gromacs. So I would like to have electrostatic interactions as
>>> other systems, so are
>>>
>>> rlist = 0.9 (in nm)
>>> rcoulomb = 0.9 (in nm)
>>>
>>> fine while I am using PME?
>>>
>> Again, there is no standard value here and it is dictated by the
>> functional form being used. You have a custom interaction potential, even
>> if you're using normal PME alongside you have user-defined, tabulated vdW
>> interactions. Presumably there should be some evaluation of what cutoffs
>> are used to satisfy whatever the assumptions are in the parametrization of
>> your model, i.e. you need to have some target data of a known system that
>> tells you that your physical model (cutoffs and functional form) is right,
>> and then you use those same settings in whatever systems are of interest.
>>
>> -Justin
>>
>>
>> Best regards
>>>
>>> On Sun, Jan 14, 2018 at 3:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>> On 1/14/18 6:01 AM, Faezeh Pousaneh wrote:
>>>>
>>>> Hi,
>>>>> I have a system of charged hard spheres (user-potential), where the vdW
>>>>> cut-off should be diameter of my molecule 0.3479. I wonder if I chose
>>>>> rlist
>>>>> and rcoulomb correctly? (see below please)
>>>>>
>>>>> I'm not sure if anyone can tell you that. You're using custom
>>>> potentials,
>>>> so setting cutoffs is part of the parametrization of that potential
>>>> itself.
>>>>
>>>> -Justin
>>>>
>>>>
>>>> integrator = md
>>>>
>>>>> dt = 0.001
>>>>> nsteps = 30000000
>>>>> nstxout = 100000 ; save coordinates
>>>>> every 0
>>>>> ps
>>>>> nstvout = 100000 ; save velocities every
>>>>> 0
>>>>> ps
>>>>> nstlog = 100000 ; update log file every
>>>>> nstenergy = 100000 ; save energies every
>>>>> nstxtcout = 100000 ; Output frequency for xtc
>>>>> file
>>>>> xtc-precision = 100000 ; precision for xtc file
>>>>> ns_type = grid ; search neighboring grid
>>>>> cells
>>>>> nstlist = 10 ; fs
>>>>> pbc = xyz ; 3-D PBC
>>>>> rlist = 0.9 ; short-range
>>>>> neighbor-list
>>>>> cutoff (in nm)
>>>>> rcoulomb = 0.9 ; short-range electrostatic
>>>>> cutoff
>>>>> (in nm)
>>>>> rvdw = 0.3479 ; short-range van der Waals
>>>>> cutoff
>>>>> (in nm)
>>>>> coulombtype = PME-user ; Particle Mesh Ewald
>>>>> for
>>>>> long-range electrostatics
>>>>> pme_order = 4 ; cubic interpolation
>>>>> fourierspacing = 0.16 ; grid spacing for FFT
>>>>> vdw-type = user
>>>>> Tcoupl = berendsen ; modified Berendsen
>>>>> thermostat
>>>>> tc-grps = co2 rest ; two coupling
>>>>> groups -
>>>>> more accurate
>>>>> tau_t = 0.1 0.1 ; time constant, in ps
>>>>> ref_t = 179.8 179.8 ; reference temperature,
>>>>> one
>>>>> for
>>>>> each group, in K
>>>>> ;tc-grps = system
>>>>> cutoff-scheme =group
>>>>> energygrps = co2 rest
>>>>> Pcoupl = berendsen ;Parrinello-Rahman
>>>>> Pcoupltype = Isotropic
>>>>> tau_p = 1.0
>>>>> compressibility = 6.2e-5
>>>>> ref_p = 5500.0
>>>>> gen_vel = yes
>>>>> gen_temp = 179.8
>>>>> gen_seed = 712349
>>>>> DispCorr =no; EnerPres ; account for cut-off vdW
>>>>> scheme
>>>>> constraints = all-bonds ; all bonds constrained
>>>>> (fixed
>>>>> length)
>>>>> continuation = no ; Restarting after NPT
>>>>> constraint-algorithm = lincs ; holonomic constraints
>>>>> lincs_iter = 1 ; accuracy of LINCS
>>>>> lincs_order = 4 ; also related to accuracy
>>>>> Best regards
>>>>>
>>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Virginia Tech Department of Biochemistry
>>>>
>>>> 303 Engel Hall
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/Support
>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 14 Jan 2018 11:32:22 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] rlist
> Message-ID: <4fbf335a-a650-3b26-1f64-1b4495bd49d2 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 1/14/18 11:29 AM, Faezeh Pousaneh wrote:
>> Thank you Justin, now I understood. However, I do not have any target data
>> for my system. What do you suggest? the longer rcoulomb is safer, right?
> Not necessarily. Longer cutoffs do not imply greater accuracy, nor does
> any specific value. It depends on your model. You have to demonstrate to
> a skeptical audience that your methods are sound. That requires
> describing a known system and its structure, energetics, and dynamics.
> Then you can move to predicting unknowns. Without that, there's no
> control to determine if your work is meaningful or a random number
> generator.
>
> -Justin
>
>> Best regards
>>
>>
>> On Sun, Jan 14, 2018 at 4:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>> On 1/14/18 10:42 AM, Faezeh Pousaneh wrote:
>>>
>>>> Thanks Justin. But I only define vdW potential form, coulomb potential
>>>> form
>>>> is as in Gromacs. So I would like to have electrostatic interactions as
>>>> other systems, so are
>>>>
>>>> rlist = 0.9 (in nm)
>>>> rcoulomb = 0.9 (in nm)
>>>>
>>>> fine while I am using PME?
>>>>
>>> Again, there is no standard value here and it is dictated by the
>>> functional form being used. You have a custom interaction potential, even
>>> if you're using normal PME alongside you have user-defined, tabulated vdW
>>> interactions. Presumably there should be some evaluation of what cutoffs
>>> are used to satisfy whatever the assumptions are in the parametrization of
>>> your model, i.e. you need to have some target data of a known system that
>>> tells you that your physical model (cutoffs and functional form) is right,
>>> and then you use those same settings in whatever systems are of interest.
>>>
>>> -Justin
>>>
>>>
>>> Best regards
>>>> On Sun, Jan 14, 2018 at 3:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>> On 1/14/18 6:01 AM, Faezeh Pousaneh wrote:
>>>>>
>>>>> Hi,
>>>>>> I have a system of charged hard spheres (user-potential), where the vdW
>>>>>> cut-off should be diameter of my molecule 0.3479. I wonder if I chose
>>>>>> rlist
>>>>>> and rcoulomb correctly? (see below please)
>>>>>>
>>>>>> I'm not sure if anyone can tell you that. You're using custom
>>>>> potentials,
>>>>> so setting cutoffs is part of the parametrization of that potential
>>>>> itself.
>>>>>
>>>>> -Justin
>>>>>
>>>>>
>>>>> integrator = md
>>>>>
>>>>>> dt = 0.001
>>>>>> nsteps = 30000000
>>>>>> nstxout = 100000 ; save coordinates
>>>>>> every 0
>>>>>> ps
>>>>>> nstvout = 100000 ; save velocities every
>>>>>> 0
>>>>>> ps
>>>>>> nstlog = 100000 ; update log file every
>>>>>> nstenergy = 100000 ; save energies every
>>>>>> nstxtcout = 100000 ; Output frequency for xtc
>>>>>> file
>>>>>> xtc-precision = 100000 ; precision for xtc file
>>>>>> ns_type = grid ; search neighboring grid
>>>>>> cells
>>>>>> nstlist = 10 ; fs
>>>>>> pbc = xyz ; 3-D PBC
>>>>>> rlist = 0.9 ; short-range
>>>>>> neighbor-list
>>>>>> cutoff (in nm)
>>>>>> rcoulomb = 0.9 ; short-range electrostatic
>>>>>> cutoff
>>>>>> (in nm)
>>>>>> rvdw = 0.3479 ; short-range van der Waals
>>>>>> cutoff
>>>>>> (in nm)
>>>>>> coulombtype = PME-user ; Particle Mesh Ewald
>>>>>> for
>>>>>> long-range electrostatics
>>>>>> pme_order = 4 ; cubic interpolation
>>>>>> fourierspacing = 0.16 ; grid spacing for FFT
>>>>>> vdw-type = user
>>>>>> Tcoupl = berendsen ; modified Berendsen
>>>>>> thermostat
>>>>>> tc-grps = co2 rest ; two coupling
>>>>>> groups -
>>>>>> more accurate
>>>>>> tau_t = 0.1 0.1 ; time constant, in ps
>>>>>> ref_t = 179.8 179.8 ; reference temperature,
>>>>>> one
>>>>>> for
>>>>>> each group, in K
>>>>>> ;tc-grps = system
>>>>>> cutoff-scheme =group
>>>>>> energygrps = co2 rest
>>>>>> Pcoupl = berendsen ;Parrinello-Rahman
>>>>>> Pcoupltype = Isotropic
>>>>>> tau_p = 1.0
>>>>>> compressibility = 6.2e-5
>>>>>> ref_p = 5500.0
>>>>>> gen_vel = yes
>>>>>> gen_temp = 179.8
>>>>>> gen_seed = 712349
>>>>>> DispCorr =no; EnerPres ; account for cut-off vdW
>>>>>> scheme
>>>>>> constraints = all-bonds ; all bonds constrained
>>>>>> (fixed
>>>>>> length)
>>>>>> continuation = no ; Restarting after NPT
>>>>>> constraint-algorithm = lincs ; holonomic constraints
>>>>>> lincs_iter = 1 ; accuracy of LINCS
>>>>>> lincs_order = 4 ; also related to accuracy
>>>>>> Best regards
>>>>>>
>>>>>> --
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Assistant Professor
>>>>> Virginia Tech Department of Biochemistry
>>>>>
>>>>> 303 Engel Hall
>>>>> 340 West Campus Dr.
>>>>> Blacksburg, VA 24061
>>>>>
>>>>> jalemkul at vt.edu | (540) 231-3129
>>>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
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>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalemkul at vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
>
> ------------------------------
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> End of gromacs.org_gmx-users Digest, Vol 165, Issue 52
> ******************************************************
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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