[gmx-users] Is gromacs-4.0.2 finally released?
Hi all, I found that gromacs-4.0.2.tar.gz under ftp.gromacs.org/pub/gromacs for a while, but now it is no longer there. Is this version finally and officially released? Regards, Jian ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] atom name in pdb converted by editconf (gmx4)
Hi, I found that when the output format from editconf (gmx4) is PDB, atom name like H5'1 will be changed to 1H5'. For other four-character atom name like ABCD, editconf works properly. example: editconf -f a.pdb -o b.pdb = a.pdb == ATOM 1 PDT 1 -1.848 4.613 1.141 1.00 0.00 ATOM 2 O1P DT 1 -2.880 4.343 2.135 1.00 0.00 ATOM 3 O2P DT 1 -0.455 4.129 1.433 1.00 0.00 ATOM 4 O5' DT 1 -2.282 4.044 -0.246 1.00 0.00 ATOM 5 C5' DT 1 -3.668 4.059 -0.487 1.00 0.00 ATOM 6 H5'1 DT 1 -3.929 4.396 -1.500 1.00 0.00 ATOM 7 H5'2 DT 1 -4.303 4.601 0.280 1.00 0.00 = b.pdb == ATOM 1 PDT 1 1.100 4.615 1.808 1.00 0.00 ATOM 2 O1P DT 1 2.094 4.346 2.840 1.00 0.00 ATOM 3 O2P DT 1 1.393 4.130 0.416 1.00 0.00 ATOM 4 O5' DT 1 -0.287 4.047 2.242 1.00 0.00 ATOM 5 C5' DT 1 -0.528 4.063 3.628 1.00 0.00 ATOM 6 1H5' DT 1 -1.541 4.400 3.889 1.00 0.00 ATOM 7 2H5' DT 1 0.239 4.606 4.263 1.00 0.00 editconf in gmx3 works fine in the above situation. Regards, Jian ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] m) Re: modify bondfree.c and recompile
Hi Berk and Mark, Thank you all for the suggestions. I will follow the safe way (make under src or top-level dir). > Date: Thu, 23 Oct 2008 02:29:14 +1100 > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Re: modify bondfree.c and recompile > To: Discussion list for GROMACS users > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Jian Zou wrote: >> Hi Mark, David and Bess, >> >> Thank you all for the suggestions. >> >> >> I know the dependency has to be somewhere in the Makefiles or the >> files they include but I cannot find it. What I am doing is simply >> "make" under top-level source directory followed by make install. In >> this case, the content of all the files (except the RC files) under >> bin and lib will be rebuild and differ from the previous build, even >> from the same source. > > Great. So what's the problem? I assume Gromacs put time stamp in the content of library and binary. If this is true, it is difficult to identify whether the difference comes from the change in the source or only from the time stamp. Regards, Jian ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: modify bondfree.c and recompile
Hi Mark, David and Bess, Thank you all for the suggestions. I know the dependency has to be somewhere in the Makefiles or the files they include but I cannot find it. What I am doing is simply "make" under top-level source directory followed by make install. In this case, the content of all the files (except the RC files) under bin and lib will be rebuild and differ from the previous build, even from the same source. Berk told me to do "make" in src/gmxlib. I checked the top-level Makefile and the the rules for "make mdrun" is "make" under src/gmxlib, src/mdlib and src/kernel, so it seems for my case "make mdrun" then "make install-mdrun" should be enough to update the binary, but how about the library? The potential I am working is 1D only instead of 3D, therefore the tabulated bonded/nonbond potential may not apply to my problem. "Walls" with wall_type=table in gmx4 could be a solution. But I do not find the implementation details like Chapter 6.7 for tabulated nonbond interaction, and therefore do not know how to make interactions of each atomtype with the wall different. Hi Yang He, I started from Appendix B.4, where the files to be modified for bonded potential are listed (Files No.6 and No.12 are the same). You may also have a look at include/physics.h and include/vec.h. Regards, Jian On Wed, Oct 22, 2008 at 3:40 AM, <[EMAIL PROTECTED]> wrote: > > Message: 1 > Date: Wed, 22 Oct 2008 11:57:46 +1100 > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] modify bondfree.c and recompile > To: Discussion list for GROMACS users > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Jian Zou wrote: >> Hi, >> >> If I only change some functional form in bondfree.c (the number of >> parameters are kept the same), can I just do "make mdrun" and "make >> install-mdrun" to recompile from the source? >> >> I cannot find the dependency between the source files and the Gromacs >> utilities (grompp and mdrun). > > It's there in the Makefiles, but you don't need to know about it. Just > use make (or just make mdrun) from the top-level source directory. > >> I compare the tpr file generated before and after the change and they >> are the same. Therefore it seems to me that grompp does not read the >> formulation of bonded interactions, am I right? > > grompp isn't changing, so its output is the same. All it does is > interpret the contents of your .top file and tell mdrun which function > to use. > > Mark > Message: 5 > Date: Wed, 22 Oct 2008 08:09:17 +0200 > From: David van der Spoel <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] modify bondfree.c and recompile > To: Discussion list for GROMACS users > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > He, Yang wrote: >> Hi Jian, >> >> Do you also need to change the source code to get a new potential function? >> I am also engaged in this job. DO you have any experience about this job? >> >> > You can use tables for bonded potentials as well, without changing any code. > >> Regards, >> >> Yang >> >> From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Jian Zou [EMAIL >> PROTECTED] >> Sent: Tuesday, October 21, 2008 7:24 AM >> To: [EMAIL PROTECTED]; gmx-users@gromacs.org >> Subject: [gmx-users] modify bondfree.c and recompile >> >> Hi, >> >> If I only change some functional form in bondfree.c (the number of >> parameters are kept the same), can I just do "make mdrun" and "make >> install-mdrun" to recompile from the source? >> >> I cannot find the dependency between the source files and the Gromacs >> utilities (grompp and mdrun). >> >> I compare the tpr file generated before and after the change and they >> are the same. Therefore it seems to me that grompp does not read the >> formulation of bonded interactions, am I right? >> >> Thank you very much for the reply. >> >> >> Regards, >> >> Jian >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.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 [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>
[gmx-users] modify bondfree.c and recompile
Hi, If I only change some functional form in bondfree.c (the number of parameters are kept the same), can I just do "make mdrun" and "make install-mdrun" to recompile from the source? I cannot find the dependency between the source files and the Gromacs utilities (grompp and mdrun). I compare the tpr file generated before and after the change and they are the same. Therefore it seems to me that grompp does not read the formulation of bonded interactions, am I right? Thank you very much for the reply. Regards, Jian ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Howto output from bondfree.c
Hi all, I am trying to modify the functional form of a bonding interaction in bondfree.c and how to output from this source file if I want to check the value of some variable? I tried printf or fprintf following fopen, neither works. Any suggestion is highly appreciated. Regards, Jian ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 48, Issue 97
Though it is trivial, did you check if mpich/lam/openmpi is compiled by icc and icc in PATH is the one you want? Did you try icc9 and fftw3 and get the same error? Regards, Jian > Message: 7 > Date: Mon, 28 Apr 2008 12:24:04 +1000 > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Need help with installation on Itanium2 > To: Discussion list for GROMACS users > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > I get the same issue with GROMACS 3.3.2 and 3.3.3 on my Itanium2 system > using Intel 10.1 icc, and I also get them even without --enable-mpi, e.g. > > ../configure --program-suffix=_3.3.3_single --with-fft=fftw2 > --with-external-blas --with-external-lapack > LIBS="-L/opt/fftw-2.1.5/intel-9.1/lib -lscs" > > then make gives > > /bin/sh ../../../../libtool --mode=compile icc -DHAVE_CONFIG_H -I. > -I../../../../src > -I../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single > -I../../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" > -O3 -w -funroll-all-loops -MT nb_kernel010_ia64_single.lo -MD -MP -MF > .deps/nb_kernel010_ia64_single.Tpo -c -o nb_kernel010_ia64_single.lo > > ../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single/nb_kernel010_ia64_single.S > icc -DHAVE_CONFIG_H -I. -I../../../../src > -I../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single > -I../../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" > -O3 -w -funroll-all-loops -MT nb_kernel010_ia64_single.lo -MD -MP -MF > .deps/nb_kernel010_ia64_single.Tpo -c > > ../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single/nb_kernel010_ia64_single.S > -o nb_kernel010_ia64_single.o > /tmp/iccEJOKXd.s(1) : error A2040: Unexpected token: Unary Diez Operator > at: Start > ...etc > > Running the above icc by hand with -O0 also fails in the same way. > > Mark > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 48, Issue 67
set sel [atomselect $molid "selection"]
for {set iframe 0} {$iframe < $nframe} {incr iframe} {
$sel frame $iframe
$sel update
$sel get {the property you want}
}
you may go to vmd mailing list for more details.
> Message: 1
> Date: Tue, 22 Apr 2008 10:42:56 +0800
> From: Dechang Li <[EMAIL PROTECTED]>
> Subject: [gmx-users] Re: the number of water molecules (Jian Zou)
> To: "gmx-users@gromacs.org"
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset="gb2312"
>
>
> >
> >Message: 2
> >Date: Mon, 21 Apr 2008 10:43:27 -0400
> >From: "Jian Zou" <[EMAIL PROTECTED]>
> >Subject: [gmx-users] Re: the number of water molecules
> >To: gmx-users@gromacs.org
> >Message-ID:
> > <[EMAIL PROTECTED]>
> >Content-Type: text/plain; charset=ISO-8859-1
> >
> >How about using vmd selection "within" to do this
>
> I have tried this. However, vmd can tell me the number in this
> frame, but there are about 5000 frames! I am tring to write a script
> to let vmd explore the results to a file VS. frames. If I make
> any progress, let you know. ^_^
>
>
> >
> >> Message: 3
> >> Date: Sun, 20 Apr 2008 21:01:57 +0800
> >> From: Dechang Li <[EMAIL PROTECTED]>
> >> Subject: [gmx-users] the number of water molecules
> >> To: "gmx-users"
> >> Message-ID: <[EMAIL PROTECTED]>
> >> Content-Type: text/plain; charset="gb2312"
> >>
> >> Dear all,
> >>
> >> How can I calculate the number of water molecules around the
> >> protein with a distance about 5 angstrom? Is that possible in
> >> Gromacs?
> >>
> >>
> >>
> >> Best regards,
> >>
> >> 2008-4-20
> >>
> >>
> >> =
> >> Dechang Li, PhD Candidate
> >> Department of Engineering Mechanics
> >> Tsinghua University
> >> Beijing 100084
> >> PR China
> >>
> >> Tel: +86-10-62773779(O)
> >> Email: [EMAIL PROTECTED]
> >> =
> >>
> >
> >
> >--
___
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[gmx-users] Re: the number of water molecules
How about using vmd selection "within" to do this > Message: 3 > Date: Sun, 20 Apr 2008 21:01:57 +0800 > From: Dechang Li <[EMAIL PROTECTED]> > Subject: [gmx-users] the number of water molecules > To: "gmx-users" > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="gb2312" > > Dear all, > > How can I calculate the number of water molecules around the > protein with a distance about 5 angstrom? Is that possible in > Gromacs? > > > > Best regards, > > 2008-4-20 > > > = > Dechang Li, PhD Candidate > Department of Engineering Mechanics > Tsinghua University > Beijing 100084 > PR China > > Tel: +86-10-62773779(O) > Email: [EMAIL PROTECTED] > = > ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: g_hbond
Hi David, Thank you for the explanation. Regards, Jian Zou - Original Message - Date: Fri, 11 Aug 2006 08:24:54 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Re: g_hbond To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jian Zou wrote: > Hi David, > > I read your JPCB paper (JPCB-110-4393) and it says that the geometric > criteria with DA distance and DHA angle is employed. Therefore I'm a > little > confused which angle is indeed used to determine the Hbond, HDA or DHA? > > Oops, that is wrong in the paper! It is HDA in the program. In the literature, e.g. the two papers by Starr et al. and the paper by Xu & Berne it is said that the O-H ... O should be less then thirty degrees, which is also what I wrote in my paper (DHA) however that does not make sense, because that angle is more than 90 degrees in a HB. Sorry about the confusion, but I'm sure that everyone either uses HDA or HAD. We can reproduce exactly the numbers of Xu & Berne with g_hbond for TIP4P and SPC/E. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: g_hbond
Hi David,
I read your JPCB paper (JPCB-110-4393) and it says that the geometric
criteria with DA distance and DHA angle is employed. Therefore I'm a little
confused which angle is indeed used to determine the Hbond, HDA or DHA?
Regards,
Jian Zou
David van der Spoel wrote:
> Dear David,
> ok. Now I understand HDA criterion. Can you give me a reference
> where I can find the differences between HDA criteria and OHD criteria
> and why one of them is preferable than the other?
We implemented this in order to reproduce a number of publications. It
is difficult to say that one is to be preferred over the other. If
something an energy-based criterium could be preferred, however
classical mechanics is not good enough to quantitatively describe the
details of hydrogen bonding anyway. Some interesting refs are:
@Article{Starr2000a,
author = {F. W. Starr and J. K. Nielsen and H. Eugene Stanley},
title = {Hydrogen-bond dynamics for the extended simple point
charge model of water},
journal = {Phys. Rev. E},
year = 2000,
volume = 62,
pages = {579-587}
}
@Article{Modig2003a,
author = {K. Modig and B. G. Pfrommer and B. Halle},
title = {Temperature-dependent hydrogen bond geometry in liquid water},
journal = {Phys. Rev. Lett.},
year = 2003,
volume = 90,
pages = 075502
}
@Article{Spoel2006b,
author = {D. van der Spoel and P. J. van Maaren and P. Larsson and
N. Timneanu},
title = {Thermodynamics of hydrogen bonding in hydrophilic and
hydrophobic media},
journal = {J. Phys. Chem. B},
year = 2006,
volume = 110,
pages = {4393-4398}
}
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