On Mon, May 31, 2010 at 10:17 PM, <gmx-users-requ...@gromacs.org> wrote:
> Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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. (xho...@sohu.com) > 6. Re: water clusters MD (Mark Abraham) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 31 May 2010 19:48:43 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] add missing atoms > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4c044adb.1000...@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 <stefh...@gmail.com> > Subject: [gmx-users] QMMM cpmd > To: gmx-users@gromacs.org > Message-ID: > <aanlktin4ubtqxd0lqpbmlzw4nqod8-bkct7xx07e7...@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" <ndhu...@andrew.cmu.edu> > Subject: [gmx-users] vibrational spectra of glucose > To: gmx-users@gromacs.org > Message-ID: > <930ba257ed1041cec9cc7a20f96fb6cf.squir...@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 <nablaobl...@yahoo.com> > Subject: Re: [gmx-users] water clusters MD > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <833755.83438...@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.abra...@anu.edu.au> wrote: > > > From: Mark Abraham <mark.abra...@anu.edu.au> > > Subject: Re: [gmx-users] water clusters MD > > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > > Date: Monday, May 31, 2010, 10:55 AM > > ----- Original Message ----- > > From: Oleksandr <nablaobl...@yahoo.com> > > Date: Monday, May 31, 2010 18:48 > > Subject: [gmx-users] water clusters MD > > To: gmx-users@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@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-requ...@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: xho...@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@gromacs.org> > Message-ID: > <1275357095.4694b653fbfe4f0e94360ff2fb9ccbe4.xho...@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.abra...@anu.edu.au> > Subject: Re: [gmx-users] water clusters MD > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <fbe2d71e2ab46.4c04f...@anu.edu.au> > Content-Type: text/plain; charset=iso-8859-1 > > ----- Original Message ----- > From: Oleksandr <nablaobl...@yahoo.com> > Date: Tuesday, June 1, 2010 11:39 > Subject: Re: [gmx-users] water clusters MD > To: Discussion list for GROMACS users <gmx-users@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.abra...@anu.edu.au> wrote: > > > > > From: Mark Abraham <mark.abra...@anu.edu.au> > > > Subject: Re: [gmx-users] water clusters MD > > > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > > > Date: Monday, May 31, 2010, 10:55 AM > > > ----- Original Message ----- > > > From: Oleksandr <nablaobl...@yahoo.com> > > > Date: Monday, May 31, 2010 18:48 > > > Subject: [gmx-users] water clusters MD > > > To: gmx-users@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@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-requ...@gromacs.org. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > > > > > -- > > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@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
-- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php