[gmx-users] Re: gmx-users Digest, Vol 74, Issue 2
manjula kasinathan
manjubfs at gmail.com
Tue Jun 1 07:29:40 CEST 2010
On Mon, May 31, 2010 at 10:17 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: add missing atoms (Justin A. Lemkul)
> 2. QMMM cpmd (Stefan Hoorman)
> 3. vibrational spectra of glucose (Nilesh Dhumal)
> 4. Re: water clusters MD (Oleksandr)
> 5. ?Fatal error in PMPI_Bcast: Other MPI error, ?..? occurs when
> using the ?particle decomposition? option. (xhomes at sohu.com)
> 6. Re: water clusters MD (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 31 May 2010 19:48:43 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] add missing atoms
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4C044ADB.1000802 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> hi
>
you can add the missing residues in the whatif server.
Manjula kasinathan.
>
> you zou wrote:
> > Hi again,
> >
> > Sorry, in "REMARK 470" there is:
> >
> > REMARK 470
> >
> > REMARK 470 MISSING ATOM
> >
> > REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
> >
> > REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
> >
> > REMARK 470 I=INSERTION CODE):
> >
> > REMARK 470 M RES CSSEQI ATOMS
> >
> > REMARK 470 SER A 2 OG
> >
> > REMARK 470 GLN A 678 CA C O &nbs
> > p; CB CG CD OE1 NE2
> >
> > REMARK 470 SER B 2 OG
> >
> > REMARK 470 GLY B 679 CA C O
> >
> > This means there are missing atoms. Is it possible to add these atoms
> > from other residue what are SER and GLN and GLY?( Copy and Paste OG from
> > other SER for example?) I think after EM these are fixed, it is true?
> >
>
> If you have several missing atoms you will have to use some external
> tool(s) to
> re-create these residues. Using cute tricks to build back one atom is easy
> enough, but re-creating a fragmented structure is much easier using tools
> designed for the task.
>
> -Justin
>
> > Thank you
> >
> >
> >> Hi everyone,<
> > br>
> >
> >> I have one question about adding atoms that are missing in residue. This
> atom is OG in SER amino acid. I don't know how can I add this atom to my
> residue. If I have to add this atom manually how can I find coordinates of
> that? Or If there is server or software to do this I will be happy if you
> suggest me its.>
> >
> > There's no automated GROMACS tool, and I haven't used any other
> particular tool for the task. For just one atom + hydrogen, you're probably
> fine to guess approximate coordinates and use EM to fix it.
> >
> >
> > ------------------------------------------------------------------------
> > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign
> > up now. <https://signup.live.com/signup.aspx?id=60969>
> >
>
> --
> ========================================
>
> 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: 2
> Date: Mon, 31 May 2010 20:49:25 -0300
> From: Stefan Hoorman <stefhoor at gmail.com>
> Subject: [gmx-users] QMMM cpmd
> To: gmx-users at gromacs.org
> Message-ID:
> <AANLkTin4UbTqXD0lQpbMlzW4NQOD8-BKcT7xX07E7Rh0 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> I've downloaded gromacs from the git repository. I type ./bootstrap
> and get loads of warnings like this
>
> configure.ac:414: warning: AC_CACHE_VAL(ac_m_cpu_7450, ...):
> suspicious cache-id, must contain _cv_ to be cached
> configure.ac:414: warning: AC_CACHE_VAL(ac_m_tune_970, ...):
> suspicious cache-id, must contain _cv_ to be cached
>
> Plus, when I type ./configure CFLAGS=-DGMX_QMMM_CPMD --with-qmmm-cpmd,
> configure runs fine except for this warning:
> configure: WARNING: unrecognized options: --with-qmmm-cpmd
>
> I figure that if ./configure does not recognize the cpmd option, there
> is no point in trying to compile gromacs with cpmd, I mean, the "make"
> command is not going to include cpmd, or is it?
> Some help on the matter would be appreciated.
> Thank you
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 31 May 2010 20:36:09 -0400
> From: "Nilesh Dhumal" <ndhumal at andrew.cmu.edu>
> Subject: [gmx-users] vibrational spectra of glucose
> To: gmx-users at gromacs.org
> Message-ID:
> <930ba257ed1041cec9cc7a20f96fb6cf.squirrel at webmail.andrew.cmu.edu>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hello,
>
> I want to calculate the normal vibrational spectra of PF6 anion.
> After the energy minimization, I found that the structure has lost his
> symmetry. It does not have Oh symetry. I compared this structre with
> ab-initio which is not matching.
> I have pasted the input file for energy minimzation.
> WHy structure is loosing its symmetry or why its not giving proper local
> minima.
> Nilesh
>
>
> define = -DFLEXIBLE
>
> constraints = none
>
> integrator = L-BFGS
>
> nsteps = 50000
>
> nbfgscorr = 50
>
> emtol = 0.0001
>
> emstep = 0.0001
>
> gen_vel = yes
>
> gen-temp = 300
>
> nstcomm = 1
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
>
> nstlist =10
>
> ; ns algorithm (simple or grid)
>
> ns-type = simple
>
> ; Periodic boundary conditions: xyz (default), no (vacuum)
>
> ; or full (infinite systems only)
>
> pbc = no
>
> ; nblist cut-off
>
> rlist = 0
>
> domain-decomposition = no
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
>
> ; Method for doing electrostatics
>
> coulombtype = Cut-Off
>
> rcoulomb-switch = 0
>
> rcoulomb = 0
>
> ; Dielectric constant (DC) for cut-off or DC of reaction field
>
>
> ; Method for doing Van der Waals
>
> vdw-type = Cut-off
>
> ; cut-off lengths
>
>
> rvdw-switch = 0
>
> rvdw = 0
>
>
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 31 May 2010 18:38:40 -0700 (PDT)
> From: Oleksandr <nablaoblada at yahoo.com>
> Subject: Re: [gmx-users] water clusters MD
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <833755.83438.qm at web113706.mail.gq1.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Look, in order to use editconf and gen box one need first to have gro and
> top files, which are generated by pdb2gmx. You say I don't need it. Ok may
> be topology file can be written by hand, but what about "gro" file?
>
> --- On Mon, 5/31/10, Mark Abraham <mark.abraham at anu.edu.au> wrote:
>
> > From: Mark Abraham <mark.abraham at anu.edu.au>
> > Subject: Re: [gmx-users] water clusters MD
> > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > Date: Monday, May 31, 2010, 10:55 AM
> > ----- Original Message -----
> > From: Oleksandr <nablaoblada at yahoo.com>
> > Date: Monday, May 31, 2010 18:48
> > Subject: [gmx-users] water clusters MD
> > To: gmx-users at gromacs.org
> >
> > > Hi,
> > > I'm new user of Gromacs. There are plenty examples how
> > to do
> > > solvation study of various proteins. But I'd like to
> > "solvate"
> > > highly ordered heavy water clusters in box of light
> > water. At
> > > the first step when I execute "pdb2gmx -f
> > watercluster.pdb" I
> > > get an error no matter which model is chosen:
> > >
> > -------------------------------------------------------
> > >
> > > Fatal error:
> > > Atom H in residue HOH 4 not found in rtp entry with 3
> > atoms
> > > while sorting atoms. Maybe
> > different protonation state.
> > > Remove this hydrogen or choose a
> > different
> > > protonation state.
> > > Option -ignh will ignore all
> > hydrogens in the input.
> > >
> > -------------------------------------------------------
> > >
> > > Can anybody help me how to solve this problem?
> >
> > You're using a tool for a different job. pdb2gmx builds a
> > topology file, mostly by constructing a [moleculetype] from
> > a polymer of repeating units. Your moleculetypes are
> > trivial, and at least one is already present in an .itp file
> > for use with #include.
> >
> > editconf and genbox make a box and fill it with generic
> > solvent. It will be simplest to either write your .top by
> > hand, or adapt an existing .top, depending what you mean by
> > "heavy water". Either way, you'll need some fluency with
> > GROMACS workflows and file types, so do all the general
> > tutorial material you can find. If you'd done so, you might
> > have realised that pdb2gmx is not really the tool for the
> > job.
> >
> > Mark
> > --
> > 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/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/mailing_lists/users.php
> >
>
>
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 01 Jun 2010 01:51:35 GMT
> From: xhomes at sohu.com
> Subject: [gmx-users] ?Fatal error in PMPI_Bcast: Other MPI error, ?..?
> occurs when using the ?particle decomposition? option.
> To: "gmx-users" <gmx-users at gromacs.org>
> Message-ID:
> <1275357095.4694b653fbfe4f0e94360ff2fb9ccbe4.xhomes at sohu.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi, everyone of gmx-users,
>
> I met a problem when I use the ‘particle decomposition’ option in a NTP
> MD simulation of Engrailed Homeodomain (En) in CL- neutralized water box. It
> just crashed with an error “Fatal error in PMPI_Bcast: Other MPI error,
> error stack: …..†. However, I’ve tried the ‘domain decomposition’
> and everything is ok! I use the Gromacs 4.05 and 4.07, the MPI lib is
> mpich2-1.2.1p1. The system box size is 5.386(nm)3. The MDP file list as
> below:
>
> ########################################################
> title = En
> ;cpp = /lib/cpp
> ;include = -I../top
> define =
> integrator = md
> dt = 0.002
> nsteps = 3000000
> nstxout = 500
> nstvout = 500
> nstlog = 250
> nstenergy = 250
> nstxtcout = 500
> comm-mode = Linear
> nstcomm = 1
>
> ;xtc_grps = Protein
> energygrps = protein non-protein
>
> nstlist = 10
> ns_type = grid
> pbc = xyz ;default xyz
> ;periodic_molecules = yes ;default no
> rlist = 1.0
>
> coulombtype = PME
> rcoulomb = 1.0
> vdwtype = Cut-off
> rvdw = 1.4
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
>
> tcoupl = v-rescale
> tc_grps = protein non-protein
> tau_t = 0.1 0.1
> ref_t = 298 298
> Pcoupl = Parrinello-Rahman
> pcoupltype = isotropic
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
>
> gen_vel = yes
> gen_temp = 298
> gen_seed = 173529
>
> constraints = hbonds
> lincs_order = 10
> ########################################################
>
> When I conduct MD using “nohup mpiexec -np 2 mdrun_dmpi -s 11_Trun.tpr -g
> 12_NTPmd.log -o 12_NTPmd.trr -c 12_NTPmd.pdb -e 12_NTPmd_ener.edr -cpo
> 12_NTPstate.cpt &†, everything is OK.
>
> Since the system doesn’t support more than 2 processes under ‘domain
> decomposition’ option, it took me about 30 days to calculate a 6ns
> trajectory. Then I decide to use the ‘particle decomposition’ option.
> The command line is “nohup mpiexec -np 6 mdrun_dmpi -pd -s 11_Trun.tpr -g
> 12_NTPmd.log -o 12_NTPmd.trr -c 12_NTPmd.pdb -e 12_NTPmd_ener.edr -cpo
> 12_NTPstate.cpt &†. And I got the crash in the nohup file like below:
> ####################
> Fatal error in PMPI_Bcast: Other MPI error, error stack:
> PMPI_Bcast(1302)......................: MPI_Bcast(buf=0x8fedeb0,
> count=60720, MPI_BYTE, root=0, MPI_COMM_WORLD) failed
> MPIR_Bcast(998).......................:
> MPIR_Bcast_scatter_ring_allgather(842):
> MPIR_Bcast_binomial(187)..............:
> MPIC_Send(41).........................:
> MPIC_Wait(513)........................:
> MPIDI_CH3I_Progress(150)..............:
> MPID_nem_mpich2_blocking_recv(948)....:
> MPID_nem_tcp_connpoll(1720)...........:
> state_commrdy_handler(1561)...........:
> MPID_nem_tcp_send_queued(127).........: writev to socket failed - Bad
> address
> rank 0 in job 25 cluster.cn_52655 caused collective abort of all ranks
> exit status of rank 0: killed by signal 9
> ####################
>
> And the ends of the log file list as below:
> ####################
> ……..
> ……..
> ……..
> ……..
> bQMMM = FALSE
> QMconstraints = 0
> QMMMscheme = 0
> scalefactor = 1
> qm_opts:
> ngQM = 0
> ####################
>
> I’ve search the gmx-users mail list and tried to adjust the md
> parameters, and no solution was found. The "mpiexec -np x" option doesn't
> work except when x=1. I did found that when the whole En protein is
> constrained using position restraints (define = -DPOSRES), the ‘particle
> decomposition’ option works. However this is not the kind of MD I want to
> conduct.
>
> Could anyone help me about this problem? And I also want to know how can I
> accelerate this kind of MD (long time simulation of small system) using
> Gromacs? Thinks a lot!
>
> (Further information about the simulated system: The system has one En
> protein (54 residues, 629 atoms), total 4848 spce waters, and 7 Cl- used to
> neutralize the system. The system has been minimized first. A 20ps MD is
> also performed for the waters and ions before EM.)
>
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 01 Jun 2010 12:16:54 +1000
> From: Mark Abraham <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] water clusters MD
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <fbe2d71e2ab46.4c04fa36 at anu.edu.au>
> Content-Type: text/plain; charset=iso-8859-1
>
> ----- Original Message -----
> From: Oleksandr <nablaoblada at yahoo.com>
> Date: Tuesday, June 1, 2010 11:39
> Subject: Re: [gmx-users] water clusters MD
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
> > Look, in order to use editconf and gen box one need first to
> > have gro and top files, which are generated by pdb2gmx. You say
>
> You need neither file for editconf and genbox. See
> http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file.
> You can use your existing correctly-formatted .pdb file.
>
> If you already have a .top for the original structure, genbox will update
> it suitably with the new waters.
>
> Mark
>
> > I don't need it. Ok may be topology file can be written by hand,
> > but what about "gro" file?
> >
> > --- On Mon, 5/31/10, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> >
> > > From: Mark Abraham <mark.abraham at anu.edu.au>
> > > Subject: Re: [gmx-users] water clusters MD
> > > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > > Date: Monday, May 31, 2010, 10:55 AM
> > > ----- Original Message -----
> > > From: Oleksandr <nablaoblada at yahoo.com>
> > > Date: Monday, May 31, 2010 18:48
> > > Subject: [gmx-users] water clusters MD
> > > To: gmx-users at gromacs.org
> > >
> > > > Hi,
> > > > I'm new user of Gromacs. There are plenty examples how
> > > to do
> > > > solvation study of various proteins. But I'd like to
> > > "solvate"
> > > > highly ordered heavy water clusters in box of light
> > > water. At
> > > > the first step when I execute "pdb2gmx -f
> > > watercluster.pdb" I
> > > > get an error no matter which model is chosen:
> > > >
> > > -------------------------------------------------------
> > > >
> > > > Fatal error:
> > > > Atom H in residue HOH 4 not found in rtp entry with 3
> > > atoms
> > > > while sorting atoms. Maybe
> > > different protonation state.
> > > > Remove this hydrogen or choose a
> > > different
> > > > protonation state.
> > > > Option -ignh will ignore all
> > > hydrogens in the input.
> > > >
> > > -------------------------------------------------------
> > > >
> > > > Can anybody help me how to solve this problem?
> > >
> > > You're using a tool for a different job. pdb2gmx builds a
> > > topology file, mostly by constructing a [moleculetype] from
> > > a polymer of repeating units. Your moleculetypes are
> > > trivial, and at least one is already present in an .itp file
> > > for use with #include.
> > >
> > > editconf and genbox make a box and fill it with generic
> > > solvent. It will be simplest to either write your .top by
> > > hand, or adapt an existing .top, depending what you mean by
> > > "heavy water". Either way, you'll need some fluency with
> > > GROMACS workflows and file types, so do all the general
> > > tutorial material you can find. If you'd done so, you might
> > > have realised that pdb2gmx is not really the tool for the
> > > job.
> > >
> > > Mark
> > > --
> > > 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/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/mailing_lists/users.php
> > >
> >
> >
> >
> >
> > --
> > 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/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/mailing_lists/users.php
>
>
> ------------------------------
>
> --
> 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/search before posting!
>
> End of gmx-users Digest, Vol 74, Issue 2
> ****************************************
>
--
With Regards,
Manjulakasinathan
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