[gmx-users] solvent group size (12548) is not a multiple of 3
Sangita Kachhap
sangita at imtech.res.in
Fri May 11 13:48:17 CEST 2012
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> Today's Topics:
>
> 1. Re: keep the nanotube cylindrical. (Elton Carvalho)
> 2. poor performance in Hemiltonian Replica Exchange (francesco oteri)
> 3. Re: poor performance in Hemiltonian Replica Exchange
> (Michael Shirts)
> 4. solvent group size (12548) is not a multiple of 3
> (Sangita Kachhap)
> 5. rvdw and DispCorr (Bernhard Knapp)
> 6. Re: solvent group size (12548) is not a multiple of 3 (Terry)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 10 May 2012 16:21:31 +0200
> From: Elton Carvalho <eltonfc at if.usp.br>
> Subject: Re: [gmx-users] keep the nanotube cylindrical.
> To: Za Pour <za.pour at yahoo.com>, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <CAOYvBoKmJs-Te_r-6uXH+k8ZMct83MmknJnucCAzfzd+WppCxA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Sat, May 5, 2012 at 7:27 PM, Za Pour <za.pour at yahoo.com> wrote:
>> Dear gmx users
>> I am simulation a system including carbon nanotube+water.I have done these
>> things:
>> However as I looked into the nvt.gro I realized that the cylindrical shape
>> of carbon nanotube
>> ?has been changed.I am not sure what I have done is correct or not?and how
>> to keep nanotube cylindrical ? any help would be really appreciated.
>> ????? Best regards
>
> I had a similar issue, but I modeled the CNT carbon atoms as opls_147,
> trying not to change the parameters too much, so I kept the bond
> lengths, angles and force constants untouched.
>
> I noticed that removing the [ dihedrals ] section from the resulting
> topology significantly reduced the tube deformation. Since g_x2top
> doesn't generate impropers and a CNT has no rotable bonds, these
> dihedrals are spurious, anyway.
>
> Also, do your tubes have open ends? If you can afford to have periodic
> tubes, so that the box z length is a multiple of the tube unit cell
> and the tube ends are bonded through the box wall, it seems much more
> stable.
> Or you could try capped tubes.
>
>
> --
> Elton Carvalho
> Tel.: +55 11 3091-6985/6922
> Dept F?sica dos Materiais e Mec?nica
> Instituto de F?sica
> Universidade de S?o Paulo
> P.O. Box 66318 - 05314-970 S?o Paulo-SP, Brazil
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 10 May 2012 18:23:54 +0200
> From: francesco oteri <francesco.oteri at gmail.com>
> Subject: [gmx-users] poor performance in Hemiltonian Replica Exchange
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CAFQcp-PpW0prmq=uuMCAJcOoEgQYwbP1=berEJ-insh_aF490Q at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear gromacs users,
>
> I performed a Hemiltonian Replica Exchange (i.e. replica exchange where
> each replica has a init_lambda=0, delta_lambda=0 and init_lambda ranging
> uniformely from 0 to 1).
>
> Since I have only ten fixed discrete lambda, I run a Temperature Replica
> Exchange where, for each replica I generated a .top file with the parameter
> rescaled through a
> python script ( in practice I did through python the same thing gromacs is
> supposed to do with the H-REM previously described). Now gromacs complained
> because
> every replica has the same setup, so I changed the temperatures using very
> close values (300.0001K,
> 300.0002K,300.0003K,300.0004K,300.0005K,300.0006K,300.0007K,300.0008K,
> 300.0009K)
> With this setup the simulation runs fine and I expect to have similar
> result.
>
> Then I compared the results observing two phenomena:
>
> 1) In the second case exchange rate is 100%, while in the first case I have
> an exchange rate close to 30%.
> Does it rise because the temperatures are too close?
>
> 2) The second setup is 3x faster!
> In particular I observe an imbalance between PME and force calculation
> ranging from 10% to 60%.
> I tried to run each replia indipendently (a different mdrun instance for
> each .tpr file) but still I observe the same performance slowdown.
> I guess the free energy impairs the efficient force calculation, but I dont
> understand why.
>
> Can someone explain me the two observations?
>
>
>
> Francesco
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> ------------------------------
>
> Message: 3
> Date: Thu, 10 May 2012 14:20:44 -0400
> From: Michael Shirts <mrshirts at gmail.com>
> Subject: Re: [gmx-users] poor performance in Hemiltonian Replica
> Exchange
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CA+zJb=g8dzPf137+uOaWhEsi57FmFW8DJF6aw--wbi3v=OwbmQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 4.6 will include Hamiltonian replia exchange functionality built into
> the MPI version.
>
> Currently the description of the error is very vague -- if you can
> write up what exactly the numbers are, and what they should be, with
> files that exactly replicate the error, then I can take a look. But
> unless I can reproduce the error you are describing out of the box,
> its unlikely I will be able to find it.
>
> Additionally, it would be easiest if the files were deposited as a
> redmine bug report, so that the information is centrally located.
>
> Best,
> Michael
>
> On Thu, May 10, 2012 at 12:23 PM, francesco oteri
> <francesco.oteri at gmail.com> wrote:
>> Dear gromacs users,
>>
>> I performed a Hemiltonian Replica Exchange (i.e. replica exchange where each
>> replica has a init_lambda=0,?delta_lambda=0 and?init_lambda ranging
>> uniformely from 0 to 1).
>>
>> Since I have only ten fixed discrete?lambda, I run a Temperature Replica
>> Exchange where, for each replica I generated a .top file with the parameter
>> rescaled through a
>> python script ( in practice I did through python the same thing gromacs is
>> supposed to do with the H-REM previously described). Now gromacs complained
>> because
>> every replica has the same setup, so I changed the temperatures using very
>> close values (300.0001K,
>> ?300.0002K,300.0003K,300.0004K,300.0005K,300.0006K,300.0007K,300.0008K,?300.0009K)
>> With this setup the simulation runs fine and I expect to have similar
>> result.
>>
>> Then I compared the results observing two phenomena:
>>
>> 1) In the second case exchange rate is 100%, while in the first case I have
>> an exchange rate close to 30%.
>> Does it rise ?because the temperatures are too close?
>>
>> 2) The second setup is 3x faster!
>> In particular I observe an imbalance between PME and force calculation
>> ranging from 10% to 60%.
>> I tried to run each replia indipendently (a different mdrun instance for
>> each .tpr file)?but still I observe the same performance slowdown.
>> I guess the free energy impairs the efficient force calculation, but I dont
>> understand why.
>>
>> Can someone explain me the two observations?
>>
>>
>>
>> Francesco
>>
>> --
>> gmx-users mailing list ? ?gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 11 May 2012 11:48:26 +0530 (IST)
> From: "Sangita Kachhap" <sangita at imtech.res.in>
> Subject: [gmx-users] solvent group size (12548) is not a multiple of 3
> To: gmx-users at gromacs.org
> Message-ID:
> <43695.172.141.121.99.1336717106.squirrel at webmail.imtech.res.in>
> Content-Type: text/plain;charset=utf-8
>
>
> Hello all
> I am runing Gromacs Tutorial KALP-15 in DPPC (I am using POPC)
> I am geeting error during addiotion of ions
> Fatal error:
> Your solvent group size (12548) is not a multiple of 3
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> I have done following:
>
> GROMACS COMMAND
>
> 1) Generate topol.top using GROMOS96 53A6 parameter set
> pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc
>
> ay prompt select 13, 2, 2
>
> 2) Download:
> * dppc128.pdb - the structure of a 128-lipid DPPC bilayer
> * dppc.itp - the moleculetype definition for DPPC
> * lipid.itp - Berger lipid parameters
>
> from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
>
> 3) Modify topol.top with:
> #include "gromos53a6.ff/forcefield.itp"
>
> to:
>
> #include "gromos53a6_lipid.ff/forcefield.itp"
>
>
> &
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include POPC chain topology
> #include "popc.itp"
>
> ; Include water topology
> #include "gromos53a6_lipid.ff/spc.itp"
>
>
>
> 4) cp files
> aminoacids.rtp
> aminoacids.hdb
> aminoacids.c.tdb
> aminoacids.n.tdb
> aminoacids.r2b
> aminoacids.vsd
> ff_dum.itp
> ffnonbonded.itp
> ffbonded.itp
> forcefield.itp
> ions.itp
> spc.itp
> watermodels.dat
>
> from gromacs top to directory named gromos53a6_lipid.ff in working directory.
> Append parameter ([ atomtypes ], [ nonbond_params ], and [ pairtypes ])from
> lipid.itp to ffnonbonded.itp & ffbonded.itp and create a forcefield.doc file
> that contains a description of the force field parameters contain "GROMOS96 53A6
> force field, extended to include Berger lipid parameters".
> Delete line ";; parameters for lipid-GROMOS interactions." and its subsequent
> line, change HW as H of [ nonbond_params ]
>
>
> 5) Generate .tpr for POPC
> grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr -maxwarn 1
> (change OW1, HW2, HW3 to OW, HW and HW2 respectively)
>
>
> 6) Remove periodicity
> trjconv -s em.tpr -f popc128a.pdb -o popc128a_whole.gro -pbc mol -ur compact
> (at command prompt select 0)
>
>
> 7) Oriant the KALP peptide within the same coordinate as written in end of
> popc128a_whole.gro
> editconf -f KALP-15_processed.gro -o KALP_newbox.gro -c -box 6.23910 6.17970
> 6.91950
>
>
> 8) Pack lipid around protein
> cat KALP_newbox.gro popc128a_whole.gro > system.gro
> Remove unnecessary lines (the box vectors from the KALP structure, the header
> information from the DPPC structure) and update the second line of the
> coordinate file (total number of atoms) accordingly.
>
>
> 9) Modify topol.top to add positional restrain on protein
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Strong position restraints for InflateGRO
> #ifdef STRONG_POSRES
> #include "strong_posre.itp"
> #endif
>
> ; Include DPPC chain topology
> #include "dppc.itp"
>
> ; Include water topology
> #include "gromos53a6_lipid.ff/spc.itp"
>
> &
>
> Genrate new positional restraint
> genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 100000 100000 100000
> (at prompt select 2)
>
> Add a line "define = -DSTRONG_POSRES" to .mdp file
>
>
>
>
> 10) Scale down lipid
> perl inflategro.pl system.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat
> system_shrink1.gro
>
>
> 11) addion POPC 128 to topol.top
>
>
> 12) Solvate with water
> Copy vdwradii.dat from Gromacs top to working directory and change the value of
> C from 0.15 to 0.375(to avoid addition of water in lipid hydrohphobic core)
>
> genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro -p
> topol.top
>
>
> grompp -f ions.mdp -c system_shrink1_solv.gro -p topol.top -o ions.tpr
>
> genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname CL -nn
> 4
> (at command prompt select 0)
>
>
>
> So can anyone please help me correct this error.
>
>
>
> With regards
> Sangita Kachhap
> SRF
> BIC,IMTECH
> CHANDIGARH
>
> ______________________________________________________________________
> ??????????????????????????�??? ???????????????????????????????????�
> ????????????????????? (??????????????????????????? ????????????????????????
> ???????????????????????? ???????????????)
> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
> ?????????????????? 39 ???, ??????????????�????????? / Sector 39-A, Chandigarh
> ????????? ?????????/PIN CODE :160036
> ??????????????????/EPABX :0172 6665 201-202
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 11 May 2012 10:23:50 +0200
> From: Bernhard Knapp <bernhard.knapp at meduniwien.ac.at>
> Subject: [gmx-users] rvdw and DispCorr
> To: gmx-users at gromacs.org
> Message-ID: <4FACCC96.8070409 at meduniwien.ac.at>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
> Dear gromacs users
>
> In a recent paper I found the following protocol of a gromacs simulation:
>
> "All simulations were performed with the GROMACS 4.0 [12] compiled in
> single-precision mode at a constant temperature of 277 K in a periodic box with
> an edge length of approximately 8.2 nm and the default GROMOS-96 43A1 forcefield
> [22]. The simulation systems each contained approximately 16,500 Simple Point
> Charge (SPC) water molecules [23]. Short-range interactions were evaluated using
> a neighbor list of 1.0 nm updated at every 10 steps. Van der Waals interactions
> used a cutoff with a smoothing
> function such that the interactions slowly decayed to zero between 0.75 nm and
> 0.90 nm. A long-range analytical dispersion correction was applied to the energy
> and pressure to account for the truncation of the Lennard-Jones interactions
> [24]. Electrostatic interactions were evaluated using the particle mesh Ewald
> (PME) [25] with a real space cutoff of 1.0 nm, a spline order of 6, a Fourier
> spacing of 0.1 m, and relative tolerance between long and short range energies
> of . All bonds to hydrogen
> were constrained with LINCS [26] with an order of 12, and a time step of 2 fs
> was used for dynamics."
>
> In the gromacs manual 4.5.4, page 104 it says: "The GROMOS-96 force field was
> parameterized with a Lennard-Jones cut-off of 1.4 nm, so be sure to use a
> Lennard-Jones cut-off (rvdw) of at least 1.4".
>
> Is it a good idea to set "DispCorr" to "EnerPres" and reduce the rvdw so
> dramatically (almost the half value)?
>
> And a second question: Is there a study on the percentage of information getting
> lost when reducing the rvdw with and without dispcorr (e.g. to 1.2, 1.0, etc) if
> the forcefield was parameterized with 1.4?
>
> best,
> Bernhard
>
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 11 May 2012 16:41:16 +0800
> From: Terry <terrencesun at gmail.com>
> Subject: Re: [gmx-users] solvent group size (12548) is not a multiple
> of 3
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CAM9kr8haSWn64DZ=AY_WcZ_kq34rmhxrwrzkAcye1jnbyVLNKA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> On Fri, May 11, 2012 at 2:18 PM, Sangita Kachhap <sangita at imtech.res.in>wrote:
>
>>
>> Hello all
>> I am runing Gromacs Tutorial KALP-15 in DPPC (I am using POPC)
>> I am geeting error during addiotion of ions
>> Fatal error:
>> Your solvent group size (12548) is not a multiple of 3
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>> I have done following:
>>
>> GROMACS COMMAND
>>
>> 1) Generate topol.top using GROMOS96 53A6 parameter set
>> pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc
>>
>> ay prompt select 13, 2, 2
>>
>> 2) Download:
>> * dppc128.pdb - the structure of a 128-lipid DPPC bilayer
>> * dppc.itp - the moleculetype definition for DPPC
>> * lipid.itp - Berger lipid parameters
>>
>> from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
>>
>> 3) Modify topol.top with:
>> #include "gromos53a6.ff/forcefield.itp"
>>
>> to:
>>
>> #include "gromos53a6_lipid.ff/forcefield.itp"
>>
>>
>> &
>>
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>>
>> ; Include POPC chain topology
>> #include "popc.itp"
>>
>> ; Include water topology
>> #include "gromos53a6_lipid.ff/spc.itp"
>>
>>
>>
>> 4) cp files
>> aminoacids.rtp
>> aminoacids.hdb
>> aminoacids.c.tdb
>> aminoacids.n.tdb
>> aminoacids.r2b
>> aminoacids.vsd
>> ff_dum.itp
>> ffnonbonded.itp
>> ffbonded.itp
>> forcefield.itp
>> ions.itp
>> spc.itp
>> watermodels.dat
>>
>> from gromacs top to directory named gromos53a6_lipid.ff in working
>> directory.
>> Append parameter ([ atomtypes ], [ nonbond_params ], and [ pairtypes ])from
>> lipid.itp to ffnonbonded.itp & ffbonded.itp and create a forcefield.doc
>> file
>> that contains a description of the force field parameters contain
>> "GROMOS96 53A6
>> force field, extended to include Berger lipid parameters".
>> Delete line ";; parameters for lipid-GROMOS interactions." and its
>> subsequent
>> line, change HW as H of [ nonbond_params ]
>>
>>
>> 5) Generate .tpr for POPC
>> grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr -maxwarn 1
>> (change OW1, HW2, HW3 to OW, HW and HW2 respectively)
>>
>>
>> 6) Remove periodicity
>> trjconv -s em.tpr -f popc128a.pdb -o popc128a_whole.gro -pbc mol -ur
>> compact
>> (at command prompt select 0)
>>
>>
>> 7) Oriant the KALP peptide within the same coordinate as written in end of
>> popc128a_whole.gro
>> editconf -f KALP-15_processed.gro -o KALP_newbox.gro -c -box 6.23910
>> 6.17970
>> 6.91950
>>
>>
>> 8) Pack lipid around protein
>> cat KALP_newbox.gro popc128a_whole.gro > system.gro
>> Remove unnecessary lines (the box vectors from the KALP structure, the
>> header
>> information from the DPPC structure) and update the second line of the
>> coordinate file (total number of atoms) accordingly.
>>
>>
>> 9) Modify topol.top to add positional restrain on protein
>>
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>>
>> ; Strong position restraints for InflateGRO
>> #ifdef STRONG_POSRES
>> #include "strong_posre.itp"
>> #endif
>>
>> ; Include DPPC chain topology
>> #include "dppc.itp"
>>
>> ; Include water topology
>> #include "gromos53a6_lipid.ff/spc.itp"
>>
>> &
>>
>> Genrate new positional restraint
>> genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 100000 100000 100000
>> (at prompt select 2)
>>
>> Add a line "define = -DSTRONG_POSRES" to .mdp file
>>
>>
>>
>>
>> 10) Scale down lipid
>> perl inflategro.pl system.gro 0.95 POPC 0 system_shrink1.gro 5
>> area_shrink1.dat
>> system_shrink1.gro
>>
>>
>> 11) addion POPC 128 to topol.top
>>
>>
>> 12) Solvate with water
>> Copy vdwradii.dat from Gromacs top to working directory and change the
>> value of
>> C from 0.15 to 0.375(to avoid addition of water in lipid hydrohphobic core)
>>
>> genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro -p
>> topol.top
>>
>>
>> grompp -f ions.mdp -c system_shrink1_solv.gro -p topol.top -o ions.tpr
>>
>> genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname
>> CL -nn 4
>> (at command prompt select 0)
>>
>
> Is group 0 your solvent? You should chose a group corresponding to the
> solvent of your system.
Thans for reply. I got it its 15 not 0, now its working fine.
>
>
>
>>
>>
>>
>> So can anyone please help me correct this error.
>>
>>
>>
>> With regards
>> Sangita Kachhap
>> SRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>> ______________________________________________________________________
>> ??????????????????????????�??? ???????????????????????????????????�
>> ????????????????????? (??????????????????????????? ????????????????????????
>> ???????????????????????? ???????????????)
>> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
>> ?????????????????? 39 ???, ??????????????�????????? / Sector 39-A, Chandigarh
>> ????????? ?????????/PIN CODE :160036
>> ??????????????????/EPABX :0172 6665 201-202
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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> before posting!
>
> End of gmx-users Digest, Vol 97, Issue 71
> *****************************************
>
Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202
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