Re: [gmx-users] question about Computational Electrophysiology
Dear Tom, the functionality of the Computational Electrophysiology module rests on exchanging ions from one compartment with water molecules from the other compartment, if the ion concentration deviates from the specified value. Keeping (also) the number of water molecules constant in the compartments would mean to take water molecules from one compartment and somehow insert them into suitable spaces found in the other compartment. This is not implemented (and also not straightforward to do, although it could probably be done…) Best, Carsten On 04 Jul 2014, at 17:40, Tom wrote: > Dear GMX developers, > > The functionality of version of 5.0 about "Computational Electrophysiology" > looks nice. > > Ions concentration can be maintaied to a fixed value. > There are options for controlling ion concentration in each compartment. > > I am wondering if water (or solvent) concentration can be kept as > a constant also? > > Thanks a lot for the help! > > Thoms > -- > 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-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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-requ...@gromacs.org.
Re: [gmx-users] Invalid order for directive atomtypes
HI Mark: thanks a lot for comments. I just played around and I noticed that I noticed that there is some invisible character inside the ligand.itp. After remove them by command dos2unix, and it works now. thx On 07/05/2014 08:54 AM, Mark Abraham wrote: A different problem can happen; the same problem can't. But we don't know what the messages were, or the link you followed, so we're stuck. Perhaps you can learn about directive order in 5.7.1 of the manual - you cannot ever have [atomtypes] after [molecules], even if they're in .itp files. Mark -- 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-requ...@gromacs.org.
Re: [gmx-users] Use trjconv in parallel
Hi Stephane, Depending on what you want to do, it may be possible to split your trajectory into frames (e.g. on /dev/shm) and process those in parallel, joining the results into a new trajectory. You can contact me if you want a python script for splitting an XTC file into frames. Cheers, Tsjerk On Wed, Jul 2, 2014 at 2:15 PM, ABEL Stephane 175950 wrote: > Thanks for your quick and also fast (;)) reply, Carsten. > > Stéphane > > > -- > > Message: 4 > Date: Wed, 2 Jul 2014 10:55:45 + > From: ABEL Stephane 175950 > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > > Subject: [gmx-users] Use trjconv in parallel, > Message-ID: > <3e39b768bb199548ab18f7289e7534af1b24f...@exdag0-b0.intra.cea.fr> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > in short : it is possible ? I use the gromacs v4.6.5. > > Thanks > > St?phane > > -- > > Message: 5 > Date: Wed, 2 Jul 2014 13:44:08 +0200 > From: Carsten Kutzner > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Use trjconv in parallel, > Message-ID: <39b862ce-6e52-4590-9c57-ba34864b2...@gwdg.de> > Content-Type: text/plain; charset=iso-8859-1 > > > On 02 Jul 2014, at 12:55, ABEL Stephane 175950 > wrote: > > > Hello, > > > > in short : it is possible ? I use the gromacs v4.6.5. > No. > > Carsten > > > > Thanks > > > > St?phane > > -- > > 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-requ...@gromacs.org. > > > > -- > > Message: 6 > Date: Wed, 02 Jul 2014 07:50:34 -0400 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] grompp does not find atomtype > Message-ID: <53b3f20a.7060...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 7/2/14, 4:40 AM, Dawid das wrote: > > I have managed to deal with this problem in following way: > > > > In topology file some bonding parameters were actually missing but some > > bonding parameters were not needed, e.g. U-B or dihedral parameters for > > atoms which are not connected, that is they belong to different parts of > my > > new residue. > > I found parameters for the missing ones and hashed (;) them out. Is it > what > > I can do? Like I say, theses bonding parameters that I hashed out were > for > > atom types which are not connected directly. > > > > Then I performed minimization with steepest descent and in output file I > > got: > > > > 4655e+05 Fmax= 6.53501e+03, atom= 1003^MStep= 426, Dmax= 2.5e-06 nm, > > Epot= -4.54655e+05 Fmax= 9.45125e+03, atom= 1003^MStep= 427, Dmax= > 1.2e-06 > > nm, Epot= -4.54655e+05 Fmax= 1.25724e+04, atom= 1003^M > > Stepsize too small, or no change in energy. > > Converged to machine precision, > > but not to the requested precision Fmax < 1000 > > > > Double precision normally gives you higher accuracy. > > You might need to increase your constraint accuracy, or turn > > off constraints alltogether (set constraints = none in mdp file) > > > > writing lowest energy coordinates. > > > > Steepest Descents converged to machine precision in 428 steps, > > but did not reach the requested Fmax < 1000. > > Potential Energy = -4.5465475e+05 > > Maximum force = 1.7057922e+04 on atom 1003 > > Norm of force = 1.1677969e+02 > > > > But I continued with NVT MD simulation. This is my nvt-md.mdp file: > > > > title = NVT MD > > integrator = md > > constraints = all-bonds > > dt = 0.001 > > nsteps = 2 > > nstenergy = 100 > > nstlist = 10 > > nstxout = 1000 > > nstvout = 1000 > > nstfout = 0 > > nstlog = 100 > > nstxtcout = 1000 > > xtcprecision= 500 > > ns_type = grid > > coulombtype = PME > > rlist = 1.0 > > rcoulomb= 1.0 > > rvdw= 1.0 > > These cutoffs are incorrect for using CHARMM force fields. See previous > posts > on proper settings. > > > tcoupl = nose-hoover > > tc-grps = Protein SOL NA > > tau_t = 0.1 0.1 0.1 ;(3 numbers -> because 3 tc-grps) > > ref_t = 100 100 100 ;(3 numbers -> because 3 tc-grps) > > Coupling water and ions separately is not sensible. > > http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do > > > Pcoupl = No > > gen_vel = yes > > gen_temp= 100 > > gen_seed= 173529 > > energygrps = Protein SOL NA > > constraint_algorithm = LINCS > > pbc = xyz > > > > And in my NVT output I got error for LINCS: > > > > relative const
Re: [gmx-users] What analysis do I need?
On 7/5/14, 6:18 AM, Batdorj Batsaikhan wrote: Dear all, I am new user, and I want to analyze conformation change of protein using MD. If you do not mind give me advice. What analysis do I need? That depends on what you define as "conformational change" - is it on the secondary or tertiary level? How to use do_dssp? Install the DSSP program, then read the manual. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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-requ...@gromacs.org.
Re: [gmx-users] Minimisation failure: The charge group moved more than the distance allowed by the domain decomposition
On 7/4/14, 5:54 AM, Vytautas Rakeviius wrote: Here all my files: https://www.dropbox.com/s/94u9b9stsk84ckz/1oyn6wat1994-15a_vconf-docking_1.tar.bz2 I try minimize this with: grompp_mpi_d -maxwarn 2 -f ~/emamber.mdp -c *_solvated_bonded_GMX.gro -p *_solvated_bonded_GMX.top -o em.tpr mdrun_mpi_d -deffnm em Here is my emamber.mdp file: http://pastebin.com/vtiuCzt0 Here is my full error: http://pastebin.com/zX57DnQf I would be thankful for help. Either the starting coordinates contain bad clashes or the topology is unstable. The initial force is not insanely high, but often CG doesn't work well as the initial minimization. Start with steepest descents and then do CG after steep has converged reasonably. Otherwise, also note that mdrun tells you the exact atom number that's having a problem; start by visualizing what's going on in its surroundings. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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-requ...@gromacs.org.
Re: [gmx-users] confout.gro
On 7/5/14, 12:51 AM, RINU KHATTRI wrote: hello gromacs users but i am confussed if confout.gro is input, in which step it is formed according to tutorial before this step the step is perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat is system_inflated.gro is confout.gro or which gro file i must be used as confout.gro perl inflategro.pl confout.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat The file "confout.gro" is the default name of the final output coordinates of an mdrun process, unless you provide a different file name to mdrun -c. In this case, the protocol is: 1. Inflate the system (produce system_inflated.gro) 2. Minimize the inflated system (produce confout.gro, unless otherwise named) 3. Begin shrinking the system, starting with the output of step 2. So "confout.gro" is the _output_ of step 2 and the _input_ of step 3. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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-requ...@gromacs.org.
Re: [gmx-users] regarding group selection in output
On 7/4/14, 12:57 AM, RINU KHATTRI wrote: hello every one now i am in trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact this command but in out put they are asking Will write gro: Coordinate file in Gromos-87 format Reading file em.tpr, VERSION 4.5.5 (single precision) Reading file em.tpr, VERSION 4.5.5 (single precision) Select group for output Group 0 ( System) has 14036 elements Group 1 ( Other) has 6656 elements Group 2 ( POPC) has 6656 elements Group 3 ( Water) has 7380 elements Group 4 (SOL) has 7380 elements Group 5 ( non-Water) has 6656 elements i am unable to understand which group to select is this command is ok or i have to use set of command to center or jump the ligand The command appears to be the same as in my membrane protein tutorial, so I'm assuming you're doing the same thing (although you're not working with the tutorial because trjconv says you have POPC, not DPPC, as the command indicates). Regardless, if you're preparing the system, you should be saving the entire system. Only saving a subset of atoms is most common for post-processing after a simulation. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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-requ...@gromacs.org.
[gmx-users] What analysis do I need?
Dear all, I am new user, and I want to analyze conformation change of protein using MD. If you do not mind give me advice. What analysis do I need? How to use do_dssp? Thank you. Batsaikhan -- 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-requ...@gromacs.org.
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 123, Issue 29
On Fri, Jul 4, 2014 at 6:19 PM, Tom wrote: > Hi Mark > > Thanks a lot for your information! > I used the newest version to compile and will have not such report about > Newest version of what? > mathcing of > Acceleration and hardware". Well, that's a start... > But the performace is still the same as before. > Then you might be doing the same thing as before, such as running the wrong mdrun. > It is slow. > about 37% peformance on Cray... > Compared to what? I did use gcc to compile but am using cray-mpich. I am wondering if > cray-mpich causes > the low performance. Or i need to change some options in the installation. > I would think not, but until you follow Justin's suggestion of sharing some complete log files (e.g. on a file-sharing service, not as email attachments) nobody can do anything. We also need to see .mdp files and a molecular description of the system. > > The following is the detail about the installation > -- > CC=gcc FC=ifort F77=ifort CXX=icpc > This is not your problem, but you should not generally mix compilers from different vendors, and definitely not mix C and C++ compilers. Mark CMAKE_PREFIX_PATH=/opt/cray/modulefiles/cray-mpich/6.3.0 > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=OFF -DGMX_MPI=ON > -DBUILD_SHARED_LIBS=off -DCMAKE_SKIP_RPATH=ON > -DCMAKE_INSTALL_PREFIX=~/App/GROMACS > make F77=gfortran > make install > -- > This is the bash_profile: > - > module swap PrgEnv-pgi PrgEnv-gnu > module load cmake > export PATH=/home/test/App/GROMACS/bin:$PATH > - > > Thanks agin for all the help! > > Thom > > > > > Message: 1 > > Date: Fri, 4 Jul 2014 10:29:07 +0200 > > From: Mark Abraham > > To: Discussion list for GROMACS users > > Cc: Discussion list for GROMACS users > > > > Subject: Re: [gmx-users] help with poor performance on gromacs on Cray > > linux > > Message-ID: > > < > > camnumasdp4g2hf9lcjwxofzygerg3idz+ag45vgpvwlouni...@mail.gmail.com> > > Content-Type: text/plain; charset=UTF-8 > > > > On Sat, Jun 28, 2014 at 11:44 PM, Tom wrote: > > > > > Dear Mark, > > > > > > Thanks a lot for your kind help! > > > I notice this on the head of *log file. > > > It is saying " > > > > > > > > > > > > > > > *Binary not matching hardware - you might be losing > > > performance.Acceleration most likely to fit this hardware: > > > AVX_128_FMAAcceleration selected at GROMACS compile time: SSE2*I > compiled > > > the gmx *tpr on the local machine and sent to the cluster. > > > > > > > That's about a factor of three you're losing. Compile for your target, > like > > the message says. > > > > > > > Please help take a look the following *log file: > > > > > > > > > - > > > > > > Log file opened on Tue Jun 17 16:13:17 2014 > > > Host: nid02116 pid: 22133 nodeid: 0 nnodes: 80 > > > Gromacs version:VERSION 4.6.5 > > > Precision: single > > > Memory model: 64 bit > > > MPI library:MPI > > > OpenMP support: enabled > > > GPU support:disabled > > > invsqrt routine:gmx_software_invsqrt(x) > > > CPU acceleration: SSE2 > > > FFT library:fftw-3.3.2-sse2 > > > Large file support: enabled > > > RDTSCP usage: enabled > > > Built on: Tue Jun 17 13:20:08 EDT 2014 > > > Built by: @***-ext5 [CMAKE] > > > Build OS/arch: Linux 2.6.32.59-0.7.2-default x86_64 > > > Build CPU vendor: AuthenticAMD > > > Build CPU brand:AMD Opteron(tm) Processor 6140 > > > Build CPU family: 16 Model: 9 Stepping: 1 > > > Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm misalignsse > mmx > > > msr nonstop_tsc pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a > > > C compiler: /opt/cray/xt-asyncpe/5.26/bin/cc GNU > > > /opt/cray/xt-asyncpe/5.26/bin/cc: INFO: Compiling with > > > CRAYPE_COMPILE_TARGET=native. > > > > > > > As discussed, the Cray compilers do not do as good a job as the > > Cray-provided gcc or icc compilers. Use those. > > > > Mark > > > > C compiler flags: -msse2-Wextra -Wno-missing-field-initializers > > > -Wno-sign-compare -Wall -Wno-unused -Wunused-value > -Wno-unused-parameter > > > -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow > > > -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 > > > -DNDEBUG > > > > > > > > > Initializing Domain Decomposition on 80 nodes > > > Dynamic load balancing: auto > > > Will sort the charge groups at every domain (re)decomposition > > > > > > NOTE: Periodic molecules are present in this system. Because of this, > the > > > domain decomposition algorithm cannot easily determine the minimum cell > > > size that it requires for treating bonded interactions. Instead, domain > > > decomposition will assume that half the non-bonded cut-off will be a > > > suitable lower bound. > > > > > > Minimum cell size due to bon
Re: [gmx-users] Helix Twist
Hi, Manual section 7.4 and 8 are good places to start with such questions. Mark On Fri, Jul 4, 2014 at 6:48 PM, Natalia Alveal F. wrote: > Dear Gromacs users, > > I work with GROMACS 4.5.4, and only want to known which tools or commands > are the best for calculate helix twist (to only one helix). > > Best regards! > > -- > Natalia Alveal Fuentealba > Ingeniera en Bioinformática > Laboratory of Membranes Proteins Structure and Signalling > Departamento de Fisiología > Pontificia Universidad Católica de Chile > Alameda 340, Santiago, Chile > Fono: 56-2-3542877 > -- > 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-requ...@gromacs.org. > -- 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-requ...@gromacs.org.
