[gmx-users] Re: Re: unwrap trajectory file using -pbc nojump
Yutian Yang
yyang18 at syr.edu
Fri Jul 5 18:59:34 CEST 2013
Hi Tsjerk,
Thanks for helping me. I can run trjconv without nojump. And when I use gmxcheck, it gives the following output:
Warning at frame 5: coordinates for atom 7035 are large (-2.14748e+06)
Warning at frame 5: coordinates for atom 7036 are large (-2.14748e+06)
Warning at frame 5: coordinates for atom 7036 are large (-2.14748e+06)
Warning at frame 5: coordinates for atom 7036 are large (-2.14748e+06)
Warning at frame 5: coordinates for atom 7037 are large (-2.14748e+06)
Warning at frame 5: coordinates for atom 7037 are large (-2.14748e+06)
Doesn't it mean my system is too large?
Thank you so much!
On Jul 4, 2013, at 3:39 AM, gmx-users-request at gromacs.org wrote:
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> Today's Topics:
>
> 1. unwrap trajectory file using -pbc nojump (Yutian Yang)
> 2. Re: unwrap trajectory file using -pbc nojump (Tsjerk Wassenaar)
> 3. Re: Re: Lennard-Jones potential for protons (Jong Wha Lee)
> 4. g_velacc (Ishwor)
> 5. Re: g_velacc (David van der Spoel)
> 6. Re: g_velacc (Ishwor)
> 7. fftw compile error for 4.6.2 (Albert)
> 8. Re: Re: g_velacc (David van der Spoel)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 3 Jul 2013 19:22:43 +0000
> From: "Yutian Yang" <yyang18 at syr.edu>
> Subject: [gmx-users] unwrap trajectory file using -pbc nojump
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID: <11CA0835-FCA9-47F9-A4CD-F6ECD6E9ABBB at syr.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear all,
>
> I want to remove PBC effects for my system and calculate the diffusion coefficient. I am using Gromacs 4.5.4. My system is a 15 nm cubic box with 376 polymer chains each with 28 beads. The simulation time is about 2000 ns. However, when I use the command
>
> trjconv_mpi -f all.xtc -s polyeqm.gro -o allnojump.xtc -pbc nojump
>
> The program stops at around 500 ns. It doesn't get killed, nor proceeds, but stuck there and I have to manually cease the program. I have tried different systems with same attributes, all with the same problem. Is it because it is a large system that makes the program running out of memory?
>
> Thank you!
>
> Yutian
>
>
>
>
>
>
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 3 Jul 2013 22:03:26 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] unwrap trajectory file using -pbc nojump
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CABzE1ShZzGY509L7Lab-1hD6ZBc=wW_=9Njss_GCA=byUQ6WaQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Yutian Yang,
>
> I don't think it's because of the size of the system. Can you run trjconv
> without -pbc nojump? And did you check the trajectory with gmxcheck? Does
> the output file exceed a maximum file size limit?
>
> Hope it helps,
>
> Tsjerk
>
>
> On Wed, Jul 3, 2013 at 9:22 PM, Yutian Yang <yyang18 at syr.edu> wrote:
>
>> Dear all,
>>
>> I want to remove PBC effects for my system and calculate the diffusion
>> coefficient. I am using Gromacs 4.5.4. My system is a 15 nm cubic box with
>> 376 polymer chains each with 28 beads. The simulation time is about 2000
>> ns. However, when I use the command
>>
>> trjconv_mpi -f all.xtc -s polyeqm.gro -o allnojump.xtc -pbc nojump
>>
>> The program stops at around 500 ns. It doesn't get killed, nor proceeds,
>> but stuck there and I have to manually cease the program. I have tried
>> different systems with same attributes, all with the same problem. Is it
>> because it is a large system that makes the program running out of memory?
>>
>> Thank you!
>>
>> Yutian
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>> 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.
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>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 4 Jul 2013 10:58:24 +0900
> From: "Jong Wha Lee" <jongwha12 at postech.ac.kr>
> Subject: [gmx-users] Re: Re: Lennard-Jones potential for protons
> To: <gmx-users at gromacs.org>
> Message-ID: <024b01ce7859$f7d97850$e78c68f0$@postech.ac.kr>
> Content-Type: text/plain; charset="us-ascii"
>
> Thank you Mark and Vitaly.
>
>
>
> I understand that simulation of protons in the solution phase is unphysical.
> Though I haven't mentioned beforehand, I'm actually trying to simulate
> noncovalent interaction between a proton and a carbonyl oxygen in the gas
> phase. Could you give me any ideas how I may simulate this?
>
>
>
> Thank you very much
>
>
>
>
>
> Jong Wha
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 3 Jul 2013 20:38:01 -0700 (PDT)
> From: Ishwor <ishwor.poudyal19 at gmail.com>
> Subject: [gmx-users] g_velacc
> To: gmx-users at gromacs.org
> Message-ID: <1372909081464-5009541.post at n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Dear all
> I have calculated the diffusion coefficient using command g_msd and I want
> to calculate diffusion coefficient using command g_velacc. I am confused
> with some terms.
> 1>I have looked the manual page of g_velacc and i found the statement "the
> time interval between data collection points is much shorter than the time
> scale of the autocorrelation." What actually does that mean?
> 2>I am also confused with the flag -acflen ( I have found that it describes
> the number of frames to be taken into consideration.Does that mean I have to
> take the points ,to integrate, in such a way that it matches with the time
> i have used in g_msd for fitting of Einsteins equation)
> 3> what does the flag -nonormalize indicates. Do I need to use it
> necessarily?
> 4>Is the command "g_analyze -f *.xvg -integrate" sufficient for
> integration?
> Ishwor
> Nepal
>
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 04 Jul 2013 07:53:12 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] g_velacc
> To: gmx-users at gromacs.org
> Message-ID: <51D50DC8.8030601 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 2013-07-04 05:38, Ishwor wrote:
>> Dear all
>> I have calculated the diffusion coefficient using command g_msd and I want
>> to calculate diffusion coefficient using command g_velacc. I am confused
>> with some terms.
>> 1>I have looked the manual page of g_velacc and i found the statement "the
>> time interval between data collection points is much shorter than the time
>> scale of the autocorrelation." What actually does that mean?
>> 2>I am also confused with the flag -acflen ( I have found that it describes
>> the number of frames to be taken into consideration.Does that mean I have to
>> take the points ,to integrate, in such a way that it matches with the time
>> i have used in g_msd for fitting of Einsteins equation)
>> 3> what does the flag -nonormalize indicates. Do I need to use it
>> necessarily?
>> 4>Is the command "g_analyze -f *.xvg -integrate" sufficient for
>> integration?
>> Ishwor
>
> Lots of good questions.
> Have you actually tried?
>
> You need to store the Velcoties quite often, maybe every 20 fs
> (depending on the system).
>> Nepal
>>
>>
>>
>> --
>> View this message in context: http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 3 Jul 2013 23:32:02 -0700 (PDT)
> From: Ishwor <ishwor.poudyal19 at gmail.com>
> Subject: [gmx-users] Re: g_velacc
> To: gmx-users at gromacs.org
> Message-ID: <1372919522806-5009543.post at n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> I have really tried to calculate diffusion coefficient using both commands
> but i cant find the comparable results.
> i have my *.mdp file as
> ;PREPROCESSING parameters
> tinit = 0
> integrator = md
> dt =.002
> nsteps = 100000000
> nstcomm = 1
>
> ;OUPUT CONTROL parameters.
> nstxout = 500
> nstvout = 500
> nstfout = 500
> nstlog = 500
> nstenergy = 500
> nstxtcout = 500
> energygrps = system
> ;NEIGHBOUR SEARCHING parameters.
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> ;ELECTROSTATIC and VdW parameters.
> rcoulomb = 1.0
> rvdw = 1.0
> epsilon-r = 1
> ;BERENDSEN TEMPERATURE COUPLING is on in two groups
> Tcoupl = berendsen
> tc-grps = system
> tau_t = 0.1
> ref_t = 303
>
> ;PRESSURE COUPLING is on
> Pcoupl = no
> gen_vel = no;
> ;BONDS parameters
> constraints = all-bonds
> constraint-algorithm = shake
> unconstrained-start = yes
> pbc = xyz
> i have calculated the diffusion coefficient using Einsteins law and found
> 2.40*10^-5 cm^2/s. I have used 2 ns time to fit the curve.
> To calculate the diffusion coefficient using g_velacc i used the command
> g_velacc -f nvt.trr -s nvt.tpr -n index.ndx -o vac.xvg -nonormalize -acflen
> 2001 -mol
> and integrate using g_analyze -f vac.xvg -integrate
> but i found the result
> Calculating the integral using the trapezium rule
> Integral 1 0.11915 +/- 0.00000
> std. dev. relative deviation of
> standard --------- cumulants from those of
> set average deviation sqrt(n-1) a Gaussian distribition
> cum. 3 cum. 4
> SS1 1.262569e-04 5.975760e-03 1.336220e-04 27.976 664.233
>
> I guess the required integral value is 0.11915 and to find diffusion
> coefficient i divide the result by 3 but get the result not matching with
> the one found using g_msd. i guess the value 0.11915 is in unit nm^2/ps.
> I dont know whether i am in the correct path or there is some problems with
> my doings.
> i am waiting for the suggestions
> Thanks
>
>
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541p5009543.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 04 Jul 2013 09:09:32 +0200
> From: Albert <mailmd2011 at gmail.com>
> Subject: [gmx-users] fftw compile error for 4.6.2
> To: gromacs maillist <gmx-users at gromacs.org>
> Message-ID: <51D51FAC.3040705 at gmail.com>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Hello:
>
> I am trying to compile Gromacs-4.6.2 for a GPU cluster with following
> command:
>
>
> CC=icc FC=ifort F77=ifort CXX=icpc
> CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw:/export/mpi/mvapich2.amd/1.4
> cmake .. -DGMX_MPI=ON
> -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs -DGMX_GPU=ON
> -DBUILD_SHARED_LIBS=OFF -DCUDA_TOOLKIT_ROOT_DIR=/export/cuda5.0
> -DFFTWF_LIBRARY= /export/fftw-3.3.3
>
> but it always claimed errors for fftw:
>
>
>
> -- Found PkgConfig: /usr/bin/pkg-config (found version "0.21")
> -- checking for module 'fftw3f'
> -- package 'fftw3f' not found
> -- pkg-config could not detect fftw3f, trying generic detection
> -- Looking for fftwf_plan_r2r_1d in /export/fftw-3.3.3/lib
> WARNING: Target "cmTryCompileExec1612346837" requests linking to
> directory "/export/fftw-3.3.3/lib". Targets may link only to
> libraries. CMake is dropping the item.
> -- Looking for fftwf_plan_r2r_1d in /export/fftw-3.3.3/lib - not found
> CMake Error at cmake/FindFFTW.cmake:97 (message):
> Could not find fftwf_plan_r2r_1d in /export/fftw-3.3.3/lib, take a
> look at
> the error message in
> /home/albert/install/gromacs-4.6.2/build/CMakeFiles/CMakeError.log to
> find
> out what went wrong. If you are using a static lib (.a) make sure
> you have
> specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
> -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
> Call Stack (most recent call first):
> CMakeLists.txt:943 (find_package)
>
>
> -- Configuring incomplete, errors occurred!
>
>
> I compiled fftw with options:
>
> ./configure CC=icc CXX=icpc F77=ifort FC=ifort
> --prefix=/home/albert/install/fftw-3.3.3 --enable-float --with-pic
> --enable-single --enable-static --enable-mpi
>
> and I don't find so called "libfftw3f.so" in the fftw installation
> directory.
>
> does anybody have any advices?
>
> THX
>
> Albert
>
>
>
> ------------------------------
>
> Message: 8
> Date: Thu, 04 Jul 2013 09:39:23 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Re: g_velacc
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <51D526AB.20705 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 2013-07-04 08:32, Ishwor wrote:
>> I have really tried to calculate diffusion coefficient using both commands
>> but i cant find the comparable results.
>> i have my *.mdp file as
>> ;PREPROCESSING parameters
>> tinit = 0
>> integrator = md
>> dt =.002
>> nsteps = 100000000
>> nstcomm = 1
>>
>> ;OUPUT CONTROL parameters.
>> nstxout = 500
>> nstvout = 500
>> nstfout = 500
>> nstlog = 500
>> nstenergy = 500
>> nstxtcout = 500
>> energygrps = system
>> ;NEIGHBOUR SEARCHING parameters.
>> nstlist = 10
>> ns_type = grid
>> rlist = 1.0
>> ;ELECTROSTATIC and VdW parameters.
>> rcoulomb = 1.0
>> rvdw = 1.0
>> epsilon-r = 1
>> ;BERENDSEN TEMPERATURE COUPLING is on in two groups
>> Tcoupl = berendsen
>> tc-grps = system
>> tau_t = 0.1
>> ref_t = 303
>>
>> ;PRESSURE COUPLING is on
>> Pcoupl = no
>> gen_vel = no;
>> ;BONDS parameters
>> constraints = all-bonds
>> constraint-algorithm = shake
>> unconstrained-start = yes
>> pbc = xyz
>> i have calculated the diffusion coefficient using Einsteins law and found
>> 2.40*10^-5 cm^2/s. I have used 2 ns time to fit the curve.
>> To calculate the diffusion coefficient using g_velacc i used the command
>> g_velacc -f nvt.trr -s nvt.tpr -n index.ndx -o vac.xvg -nonormalize -acflen
>> 2001 -mol
>> and integrate using g_analyze -f vac.xvg -integrate
>> but i found the result
>> Calculating the integral using the trapezium rule
>> Integral 1 0.11915 +/- 0.00000
>> std. dev. relative deviation of
>> standard --------- cumulants from those of
>> set average deviation sqrt(n-1) a Gaussian distribition
>> cum. 3 cum. 4
>> SS1 1.262569e-04 5.975760e-03 1.336220e-04 27.976 664.233
>>
>> I guess the required integral value is 0.11915 and to find diffusion
>> coefficient i divide the result by 3 but get the result not matching with
>> the one found using g_msd. i guess the value 0.11915 is in unit nm^2/ps.
>> I dont know whether i am in the correct path or there is some problems with
>> my doings.
>> i am waiting for the suggestions
>
> nstvout = 10
>
>> Thanks
>>
>>
>>
>>
>> --
>> View this message in context: http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541p5009543.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
>
>
> ------------------------------
>
> --
> 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!
>
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