[gmx-users] gromacs.org_gmx-users Digest, Vol 157, Issue 42
ZUO Taisen
zuots at ihep.ac.cn
Thu May 11 05:25:04 CEST 2017
Dear Sir/Madam:
Thanks for your reply! But I'm puzzled that my question "Inconsistence of SPC/E and TIP4P water in Gromacs (ZUO Taisen)" did not got any answers. Is there anything wrong?
Sincerely yours
Taisen Zuo
> -----原始邮件-----
> 发件人: gromacs.org_gmx-users-request at maillist.sys.kth.se
> 发送时间: 2017年5月11日 星期四
> 收件人: gromacs.org_gmx-users at maillist.sys.kth.se
> 抄送:
> 主题: gromacs.org_gmx-users Digest, Vol 157, Issue 42
>
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> Today's Topics:
>
> 1. Re: How to use "gmx view" on Ubuntu? (Frank Zhou)
> 2. Re: How to use "gmx view" on Ubuntu? (Frank Zhou)
> 3. Re: Regarding simulation radioactive material (Christopher Neale)
> 4. Inconsistence of SPC/E and TIP4P water in Gromacs (ZUO Taisen)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 10 May 2017 15:03:21 -0600
> From: Frank Zhou <frankzhouusa at gmail.com>
> To: <gmx-users at gromacs.org>, "gromacs.org_gmx-users"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] How to use "gmx view" on Ubuntu?
> Message-ID: <D538DADA.131AF%frankzhouusa at gmail.com>
> Content-Type: text/plain; charset="ISO-8859-1"
>
> Hello Cheng,
>
> You can firstly install libX11-devel by yourself:
> # sudo apt-get install libx11-dev (in CentOS: sudo yum install
> libX11-devel)
>
>
> Then "cd build" and run:
> # cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -DGMX_X11=on
>
>
> Thanks,
> Frank
>
>
> On 5/10/17, 2:33 PM, "Mark Abraham"
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
> mark.j.abraham at gmail.com> wrote:
>
> >Hi,
> >
> >On Wed, May 10, 2017 at 10:28 PM ZHANG Cheng <272699575 at qq.com> wrote:
> >
> >> Dear Mark,
> >> Yes, Justin gave me a link for Gromacs-2016.3, but not the link for
> >> xorg-dev.
> >>
> >
> >You don't need or want one. That's what the apt-get commands are for.
> >
> >
> >> Do you mean, I should uninstall my current Gromacs 5.0.4, then install
> >>the
> >> Gromacs-2016.3, so that I can use the "gmx view" in the Gromacs-2016.3
> >>on
> >> my Ubuntu?
> >>
> >
> >You can install whatever version you want, but generally the latest
> >version, or one with which you need scientific consistency are reasonable
> >decisions. gmx view doesn't change much, though.
> >
> >As I said in my first reply you need to compile and install some new
> >GROMACS version: "You'll need to install X11 headers and libraries (the
> >package is called xorg-dev, off the top of my head), and use cmake ..
> >-DGMX_X11=on before compiling & installing."
> >
> >Whether and how you need to uninstall your old GROMACS is dependent on it
> >was previously installed. Generally there's no need to do so, but it might
> >be a good idea.
> >
> >Mark
> >
> >Cheng
> >>
> >>
> >>
> >>
> >> ------------------ Original ------------------
> >> From: "ZHANG Cheng";<272699575 at qq.com>;
> >> Date: Thu, May 11, 2017 02:50 AM
> >> To: "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
> >>
> >> Subject: Re: Re: Re: How to use "gmx view" on Ubuntu?
> >>
> >>
> >>
> >> Dear Justin,
> >> Thank you for your link. I know how to install the Gromacs based on your
> >> link. But do you know where I can download the tar.gz file so that I can
> >> compile it and then use "gmx view"?
> >>
> >>
> >> Thank you.
> >>
> >>
> >> Cheng
> >>
> >>
> >>
> >>
> >> ------------------ Original ------------------
> >> From: "ZHANG Cheng";<272699575 at qq.com>;
> >> Date: Wed, May 10, 2017 11:27 PM
> >> To: "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
> >>
> >> Subject: Re: Re: How to use "gmx view" on Ubuntu?
> >>
> >>
> >>
> >> Dear Mark Abraham,
> >> Thank you very much for your updating.
> >>
> >>
> >> Sorry, could you please tell me where can I download the cmake file, or
> >> which command line to use, in order to compiling & installing?
> >>
> >>
> >> I have tried the below and they both worked, but "gmx view ?" still not
> >> work, with the same issue "Compiled without X-Windows - can not run
> >>viewer."
> >> ) sudo apt-get install xorg-dev
> >> ) sudo apt-get install xorg-dev libglu1-mesa-dev
> >>
> >>
> >>
> >> (Sorry, I am not sure how to find the files to download)
> >>
> >>
> >> Thank you.
> >>
> >>
> >> Yours sincerely
> >> Cheng
> >>
> >>
> >> ------------------ Original ------------------
> >> From: "ZHANG Cheng";<272699575 at qq.com>;
> >> Date: Wed, May 10, 2017 04:22 AM
> >> To: "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
> >>
> >> Subject: Re: How to use "gmx view" on Ubuntu?
> >>
> >>
> >>
> >> Dear Gromacs and Mark Abraham,
> >> Sorry, I am not familiar with compiling issue.
> >>
> >>
> >> I installed xorg-dev by:
> >> sudo apt-get install xorg-dev
> >>
> >>
> >> Then, I type
> >> cmake .. -DGMX_X11=on
> >>
> >>
> >> But I was told:
> >> CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/...
> >>..."
> >> does not appear to contain CMakeLists.txt.
> >>
> >>
> >> What I should do next?
> >>
> >>
> >> Thank you.
> >>
> >>
> >> Cheng
> >>
> >>
> >>
> >>
> >>
> >>
> >> ------------------ Original ------------------
> >> From: "ZHANG Cheng";<272699575 at qq.com>;
> >> Date: Wed, May 10, 2017 02:58 AM
> >> To: "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
> >>
> >> Subject: How to use "gmx view" on Ubuntu?
> >>
> >>
> >>
> >> Dear Gromacs,
> >> I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS.
> >>
> >>
> >> When I run "gmx view ..." as below:
> >>
> >>
> >> gmx view -f dppc-md.xtc -s dppc-md.tpr
> >>
> >>
> >> I got the following:
> >>
> >>
> >> Compiled without X-Windows - can not run viewer.
> >>
> >>
> >>
> >>
> >>
> >> Can I ask how to use "gmx view" on Ubuntu? Thank you.
> >>
> >>
> >> Yours sincerely
> >> Cheng
> >> --
> >> 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-request at 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-request at gromacs.org.
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 10 May 2017 15:03:21 -0600
> From: Frank Zhou <frankzhouusa at gmail.com>
> To: <gmx-users at gromacs.org>, "gromacs.org_gmx-users"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] How to use "gmx view" on Ubuntu?
> Message-ID: <D538DADA.131AF%frankzhouusa at gmail.com>
> Content-Type: text/plain; charset="ISO-8859-1"
>
> Hello Cheng,
>
> You can firstly install libX11-devel by yourself:
> # sudo apt-get install libx11-dev (in CentOS: sudo yum install
> libX11-devel)
>
>
> Then "cd build" and run:
> # cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -DGMX_X11=on
>
>
> Thanks,
> Frank
>
>
> On 5/10/17, 2:33 PM, "Mark Abraham"
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
> mark.j.abraham at gmail.com> wrote:
>
> >Hi,
> >
> >On Wed, May 10, 2017 at 10:28 PM ZHANG Cheng <272699575 at qq.com> wrote:
> >
> >> Dear Mark,
> >> Yes, Justin gave me a link for Gromacs-2016.3, but not the link for
> >> xorg-dev.
> >>
> >
> >You don't need or want one. That's what the apt-get commands are for.
> >
> >
> >> Do you mean, I should uninstall my current Gromacs 5.0.4, then install
> >>the
> >> Gromacs-2016.3, so that I can use the "gmx view" in the Gromacs-2016.3
> >>on
> >> my Ubuntu?
> >>
> >
> >You can install whatever version you want, but generally the latest
> >version, or one with which you need scientific consistency are reasonable
> >decisions. gmx view doesn't change much, though.
> >
> >As I said in my first reply you need to compile and install some new
> >GROMACS version: "You'll need to install X11 headers and libraries (the
> >package is called xorg-dev, off the top of my head), and use cmake ..
> >-DGMX_X11=on before compiling & installing."
> >
> >Whether and how you need to uninstall your old GROMACS is dependent on it
> >was previously installed. Generally there's no need to do so, but it might
> >be a good idea.
> >
> >Mark
> >
> >Cheng
> >>
> >>
> >>
> >>
> >> ------------------ Original ------------------
> >> From: "ZHANG Cheng";<272699575 at qq.com>;
> >> Date: Thu, May 11, 2017 02:50 AM
> >> To: "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
> >>
> >> Subject: Re: Re: Re: How to use "gmx view" on Ubuntu?
> >>
> >>
> >>
> >> Dear Justin,
> >> Thank you for your link. I know how to install the Gromacs based on your
> >> link. But do you know where I can download the tar.gz file so that I can
> >> compile it and then use "gmx view"?
> >>
> >>
> >> Thank you.
> >>
> >>
> >> Cheng
> >>
> >>
> >>
> >>
> >> ------------------ Original ------------------
> >> From: "ZHANG Cheng";<272699575 at qq.com>;
> >> Date: Wed, May 10, 2017 11:27 PM
> >> To: "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
> >>
> >> Subject: Re: Re: How to use "gmx view" on Ubuntu?
> >>
> >>
> >>
> >> Dear Mark Abraham,
> >> Thank you very much for your updating.
> >>
> >>
> >> Sorry, could you please tell me where can I download the cmake file, or
> >> which command line to use, in order to compiling & installing?
> >>
> >>
> >> I have tried the below and they both worked, but "gmx view ?" still not
> >> work, with the same issue "Compiled without X-Windows - can not run
> >>viewer."
> >> ) sudo apt-get install xorg-dev
> >> ) sudo apt-get install xorg-dev libglu1-mesa-dev
> >>
> >>
> >>
> >> (Sorry, I am not sure how to find the files to download)
> >>
> >>
> >> Thank you.
> >>
> >>
> >> Yours sincerely
> >> Cheng
> >>
> >>
> >> ------------------ Original ------------------
> >> From: "ZHANG Cheng";<272699575 at qq.com>;
> >> Date: Wed, May 10, 2017 04:22 AM
> >> To: "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
> >>
> >> Subject: Re: How to use "gmx view" on Ubuntu?
> >>
> >>
> >>
> >> Dear Gromacs and Mark Abraham,
> >> Sorry, I am not familiar with compiling issue.
> >>
> >>
> >> I installed xorg-dev by:
> >> sudo apt-get install xorg-dev
> >>
> >>
> >> Then, I type
> >> cmake .. -DGMX_X11=on
> >>
> >>
> >> But I was told:
> >> CMake Error: The source directory "/home/lanselibai/Cheng/gromacs/...
> >>..."
> >> does not appear to contain CMakeLists.txt.
> >>
> >>
> >> What I should do next?
> >>
> >>
> >> Thank you.
> >>
> >>
> >> Cheng
> >>
> >>
> >>
> >>
> >>
> >>
> >> ------------------ Original ------------------
> >> From: "ZHANG Cheng";<272699575 at qq.com>;
> >> Date: Wed, May 10, 2017 02:58 AM
> >> To: "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
> >>
> >> Subject: How to use "gmx view" on Ubuntu?
> >>
> >>
> >>
> >> Dear Gromacs,
> >> I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS.
> >>
> >>
> >> When I run "gmx view ..." as below:
> >>
> >>
> >> gmx view -f dppc-md.xtc -s dppc-md.tpr
> >>
> >>
> >> I got the following:
> >>
> >>
> >> Compiled without X-Windows - can not run viewer.
> >>
> >>
> >>
> >>
> >>
> >> Can I ask how to use "gmx view" on Ubuntu? Thank you.
> >>
> >>
> >> Yours sincerely
> >> Cheng
> >> --
> >> 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-request at 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-request at gromacs.org.
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 11 May 2017 00:16:13 +0000
> From: Christopher Neale <chris.neale at alum.utoronto.ca>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Regarding simulation radioactive material
> Message-ID:
> <YTOPR01MB05705CAA4E4B0D12D9E9B637C5ED0 at YTOPR01MB0570.CANPRD01.PROD.OUTLOOK.COM>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Unless you're using a bizarre Hamiltonian that includes mass then you should be able to change masses without affecting equilibrium thermodynamic properties at all, right? Dynamics will of course be altered. Justin's right though, any thermodynamic differences in C14 vs C12 would have to be through reparameterization and you likely couldn't trust any changes in dynamics resulting from first changing the mass.
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
> Sent: 10 May 2017 16:05:28
> To: RAHUL SURESH; Discussion list for GROMACS users
> Subject: Re: [gmx-users] Regarding simulation radioactive material
>
>
> Please keep the discussion on the gmx-users mailing list. I am not a private
> help service.
>
> On 5/10/17 2:58 PM, RAHUL SURESH wrote:
> > Dear Justin
> >
> > I would like to simulate a radioactive peptide.. I think this is the first of
> > its kind. I wish to study interaction between Radioactive peptide and a protein.
> >
> > To make it simple if I want to convert all my carbon into radioactive isotopes
> > c14, and simulate is it possible ?
> >
>
> Possible, yes, but not correct. If you change the mass of any atoms, you change
> their vibrational frequencies, which means you need to reparametrize all the
> bonded terms involving the modified atom types. That means bonds, angles, and
> dihedrals. Whether or not this gives anything meaningful in terms of modeling
> the interactions of a radioactive peptide with a larger protein is another
> question. If you're not changing any elements of the nonbonded terms (which you
> likely shouldn't) then I doubt the interactions will be different in any
> statistically meaningful way from the default parameters. Re-doing bonded
> parameters is a LOT of work.
>
> -Justin
>
> > References, I have found few experimental papers on this. Where they have Used
> > isotopes of hydrogen. Tritium instead of hydrogen.
> >
> > If any information regarding this is available, will be a great use for me.
> >
> > Thank you.
> > Sorry for writing in person
> > --
> > */Regards,/*
> > */Rahul Suresh/*
> > */Research Scholar/*
> > */Bharathiar University/*
> > */Coimbatore/*
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at 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-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 11 May 2017 09:23:43 +0800 (GMT+08:00)
> From: "ZUO Taisen" <zuots at ihep.ac.cn>
> To: "gromacs.org_gmx-users"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Inconsistence of SPC/E and TIP4P water in Gromacs
> Message-ID: <5a4a3a1f.13b1d.15bf51ac2cc.Coremail.zuots at ihep.ac.cn>
> Content-Type: text/plain; charset=GBK
>
>
> Hi guys:
>
> I have compared the SPC/E and TIP4P water of the opls force field in Gromacs.But there is something inconsistent of the potential energy in the system
>
>
> The potential energy of SPC/E water is -4.71400e+04/1000=-47.14kJ/mol which is far from the results from literature (Peter G. Kusalik, Science,vol,265,26,p1219-1221,1994)
> The potential energy TIP4P water is -4.17875e+04/1000=41.787kJ/mol which is very close to the literature -41.8kJ/mol(Peter G. Kusalik, Science,vol,265,26,p1219-1221,1994)
>
>
> I have attached all the files simulating the SPC/E and TIP4P water(.trr .xtc files are delected) and also the related paper in my last email but was suspended because of the files were too big.So no files was attached this time but the .mdp file was posted as following.
>
>
> I'm eager to know why! Thank you very much!
>
>
> TIP4P simulation results:
> Statistics over 30000001 steps using 300001 frames
>
> Energies (kJ/mol)
> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
> 7.71821e+03 -2.05973e+02 -4.93956e+04 9.58136e+01 -4.17875e+04
> Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar)
> 7.30494e+03 -3.44826e+04 2.93006e+02 -1.14009e+02 1.41117e+00
>
>
> SPC/E simulation results:
>
> Statistics over 30000001 steps using 300001 frames
>
>
> Energies (kJ/mol)
> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
> 9.23352e+03 -2.12206e+02 -5.62576e+04 9.63633e+01 -4.71400e+04
> Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar)
> 7.30494e+03 -3.98350e+04 2.93005e+02 -1.18040e+02 1.64654e+00
>
>
>
>
> title= OPLS MD waterethanol siimulation
> ; Run parameters
> integrator= md; leap-frog integrator
> nsteps= 30000000; 1 * 20000000 = 20000 ps (20 ns)
> dt = 0.001; 1 fs
> ; Output control
> nstxout = 100000; save coordinates every 10.0 ps
> nstvout = 100000; save velocities every 10.0 ps
> nstenergy = 100000; save energies every 10.0 ps
> nstlog = 100000; update log file every 10.0 ps
> nstxout-compressed = 100000 ; save compressed coordinates every 10.0 ps
> define =-DEFLEXIBLE ; flexible water
> compressed-x-grps = System ; replaces xtc-grps
> ; Bond parameters
> continuation = yes; Restarting after NPT
> constraint_algorithm = lincs ; holonomic constraints
> constraints = none; H bonds (even heavy atom-H bonds) constrained
> lincs_iter = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> cutoff-scheme = Verlet
> ns_type = grid; search neighboring grid cells
> nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
> rcoulomb = 1.2; short-range electrostatic cutoff (in nm)
> rvdw = 1.2; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME; Particle Mesh Ewald for long-range electrostatics
> pme_order = 4 ; cubic interpolation
> fourierspacing= 0.12; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl= V-rescale ; modified Berendsen thermostat
> tc-grps= SOL ; two coupling groups - more accurate
> tau_t= 0.1 ; time constant, in ps
> ref_t= 293 ; reference temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
> pcoupltype = isotropic ; uniform scaling of box vectors
> tau_p = 2.0 ; time constant, in ps
> ref_p = 1.0 ; reference pressure, in bar
> compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc= xyz; 3-D PBC
> ; Dispersion correction
> DispCorr= EnerPres; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel= no; Velocity generation is off
>
>
>
> --
>
>
> Taisen Zuo
>
> China Spallation Neutron Source?Institute of High Energy Physics? Chinese Academy of Science
> A1-510, Zhongziyuan road NO.1, Dongguan, Guangdong, PR China. 523770
> Tel: 86-0769-89156495
> Cell: 13650469795
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>
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--
Taisen Zuo
China Spallation Neutron Source，Institute of High Energy Physics， Chinese Academy of Science
A1-510, Zhongziyuan road NO.1, Dongguan, Guangdong, PR China. 523770
Tel: 86-0769-89156495
Cell: 13650469795
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