Dear community.<br><br>Thank you for your help. After doing "./configure" without problems, the system showed ERROR again after "make".Here, I put the steps that I followed, what is my error?. Please help me with your advices. By the way... I made a mistake, I am using Rocks cluster 5.4.<br>
<br>root@bioinfocluster gromacs-4.5.4]# mpi-selector-menu <div>Current system default: openmpi-1.4-gcc-x86_64</div><div>Current user default: <none></div><div><br></div><div> "u" and "s" modifiers can be added to numeric and "U"</div>
<div> commands to specify "user" or "system-wide".</div><div><br></div><div>1. openmpi-1.4-gcc-i386</div><div>2. openmpi-1.4-gcc-x86_64</div><div>3. rocks-openmpi-1.4.1</div><div>4. sun-ct-8.2.1-i386</div>
<div>5. sun-ct-8.2.1-x86_64</div><div>U. Unset default</div><div>Q. Quit</div><div><br></div><div>Selection (1-5[us], U[us], Q): </div><div><br></div><div><br></div><div><span class="yiv2031717814Apple-style-span" style="font-size: 10px; line-height: 16px;"><ol start="1" class="yiv2031717814dp-sh" style="margin: 0px 0px 1px 45px ! important; padding: 0px; line-height: 16px; border-style: none; font-size: 11px; list-style-type: decimal; background-color: rgb(255, 255, 255);">
<li class="yiv2031717814alt" style="margin: 0px ! important; padding: 0px 3px 0px 10px ! important; border-style: none none none solid; font-size: 11px; list-style-type: decimal-leading-zero; list-style-position: outside; border-left: 3px solid rgb(108, 226, 108); background-color: rgb(255, 255, 255); color: inherit; line-height: 14px;">
<span style="margin: 0px; padding: 0px; border-style: none; font-size: 11px; color: black; background-color: inherit;"><span class="yiv2031717814command" style="margin: 0px; padding: 0px; border-style: none; font-size: 11px; color: rgb(100, 100, 100); background-color: inherit; font-weight: bold;">export</span><span style="margin: 0px; padding: 0px; border-style: none; font-size: 11px; color: black; background-color: inherit;"> CPPFLAGS=</span><span class="yiv2031717814string" style="margin: 0px; padding: 0px; border-style: none; font-size: 11px; color: blue; background-color: inherit;">"-I/opt/rocks/include"</span><span style="margin: 0px; padding: 0px; border-style: none; font-size: 11px; color: black; background-color: inherit;"> </span></span></li>
<li class="yiv2031717814alt" style="margin: 0px ! important; padding: 0px 3px 0px 10px ! important; border-style: none none none solid; font-size: 11px; list-style-type: decimal-leading-zero; list-style-position: outside; border-left: 3px solid rgb(108, 226, 108); background-color: rgb(255, 255, 255); color: inherit; line-height: 14px;">
<span style="margin: 0px; padding: 0px; border-style: none; font-size: 11px; color: black; background-color: inherit;"><span style="margin: 0px; padding: 0px; border-style: none; font-size: 11px; color: black; background-color: inherit;"></span></span><span class="yiv2031717814command" style="margin: 0px; padding: 0px; border-style: none; font-size: 11px; color: rgb(100, 100, 100); background-color: inherit; font-weight: bold;">export</span><span style="margin: 0px; padding: 0px; border-style: none; font-size: 11px; color: black; background-color: inherit;"> LDFLAGS=</span><span class="yiv2031717814string" style="margin: 0px; padding: 0px; border-style: none; font-size: 11px; color: blue; background-color: inherit;">"-L/opt/rocks/lib"</span><span style="margin: 0px; padding: 0px; border-style: none; font-size: 11px; color: black; background-color: inherit;"> </span></li>
<li class="yiv2031717814alt" style="margin: 0px ! important; padding: 0px 3px 0px 10px ! important; border-style: none none none solid; font-size: 11px; list-style-type: decimal-leading-zero; list-style-position: outside; border-left: 3px solid rgb(108, 226, 108); background-color: rgb(255, 255, 255); color: inherit; line-height: 14px;">
<span style="margin: 0px; padding: 0px; border-style: none; font-size: 11px; color: black; background-color: inherit;"> </span></li><li class="yiv2031717814" style="margin: 0px ! important; padding: 0px 3px 0px 10px ! important; border-style: none none none solid; font-size: 11px; list-style-type: decimal-leading-zero; list-style-position: outside; border-left: 3px solid rgb(108, 226, 108); background-color: rgb(248, 248, 248); color: rgb(92, 92, 92); line-height: 14px;">
<span style="margin: 0px; padding: 0px; border-style: none; font-size: 11px; color: black; background-color: inherit;">./configure --<span class="yiv2031717814command" style="margin: 0px; padding: 0px; border-style: none; font-size: 11px; color: rgb(100, 100, 100); background-color: inherit; font-weight: bold;">enable</span><span style="margin: 0px; padding: 0px; border-style: none; font-size: 11px; color: black; background-color: inherit;">-mpi --prefix=/share/apps/opt/gromacs </span></span></li>
</ol></span></div><div><b><br></b></div><div><b>Until this point, I did not have errors, then...</b><br></div><div><br></div><div># make</div><div>....</div><div>make[3]: *** [<a rel="nofollow" target="_blank" href="http://libmd.la/">libmd.la</a>] Error 1</div>
<div>make[3]: Leaving directory `/share/apps/src/gromacs-4.5.4/src/mdlib'</div>
<div>make[2]: *** [all-recursive] Error 1</div><div>make[2]: Leaving directory `/share/apps/src/gromacs-4.5.4/src'</div><div>make[1]: *** [all] Error 2</div><div>make[1]: Leaving directory `/share/apps/src/gromacs-4.5.4/src'</div>
<div>make: *** [all-recursive] Error 1</div><br><b>Thanks in advance.<br><br>Miguel.</b><br><br><br><br><br><div class="gmail_quote">2011/4/11 <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span><br>
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Today's Topics:<br>
<br>
1. Re: comm-grps for a membrane-protein-ligand system<br>
(Justin A. Lemkul)<br>
2. Re: How to install GROMACS in Rocks Cluster 4.5.4 : ERROR<br>
(Justin A. Lemkul)<br>
3. Re: g_hbond (Erik Marklund)<br>
4. Pressure coupling problem (Fabian Casteblanco)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 11 Apr 2011 13:58:24 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] comm-grps for a membrane-protein-ligand<br>
system<br>
To: "Gromacs Users' List" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DA34140.6040103@vt.edu">4DA34140.6040103@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Peter C. Lai wrote:<br>
> Ok thanks<br>
><br>
> My primary concern is to cancel membrane-protein drift - the protein<br>
> getting pushed to one side of the membrane box (also it's important for<br>
> me to have the protein stay centered in the box too). I have not seen<br>
<br>
There is no "center" to a periodic system. Molecules diffuse, there's no way<br>
around it. If you try to apply some biasing force to fit some visualization<br>
convenience, you're potentially damaging the simulation's integrity.<br>
<br>
> stability issues otherwise with COM turned on in the case of the unbound<br>
> protein and the membrane as separate COM groups. The only instability<br>
> I have encountered thus far is LINCS crashing due to too much forces if<br>
> I set the restraint forces too high (like 100000 kJ/mol), but I've resigned<br>
> myself to the fact that the residual RMS drift appears acceptable at the end<br>
> of membrane/solvent equilibration runs if I drop it down to 10000 kJ/mol<br>
> during NPT equilibration).<br>
<br>
Position restraints do not fix anything in place, they merely provide an energy<br>
barrier that penalizes change. If your goal is simply to obtain a reasonably<br>
equilibrated system, then there is no need for a force constant above about<br>
1000, otherwise you may be overtly influencing the ability of your system to<br>
respond to change.<br>
<br>
-Justin<br>
<br>
><br>
> On 2011-04-11 07:00:39AM -0500, Justin A. Lemkul wrote:<br>
>><br>
>> Peter C. Lai wrote:<br>
>>> Should I couple a ligand associated with a membrane protein to the same<br>
>>> COM group as the Protein_POPC group? It makes sense to me that would be the<br>
>>> case since if we are investigating the interaction between protein+membrane<br>
>>> and ligand we want to have the same COM correction vector applied to both<br>
>>> relative to SOL_Ions but I just wanted to make sure...<br>
>>><br>
>> If specifying multiple groups for COM motion removal, yes, the intuitive<br>
>> solution is to group the ligand with the protein (since they're physically<br>
>> bound, presumably). The general complication is whether or not multiple COM<br>
>> groups are necessary - if the protein protrudes out into the solvent in any<br>
>> substantial way, you could have instability when the solvent and<br>
>> protein/membrane COMs get re-set. I have seen this before in the case of a<br>
>> protein in water with separate COM groups (which is not appropriate, for the<br>
>> record). Membrane systems are somewhat more complicated because they form<br>
>> interfaces that can slide, but if the protein somehow affects this behavior,<br>
>> well, I don't know that there's a trivial solution other than "comm_grps =<br>
>> System" to avoid possible instability. If you're interested in<br>
>> diffusion-related properties, on the other hand, that may not be appropriate.<br>
>> Plenty to think about, but again, probably no "easy" solution.<br>
>><br>
>> -Justin<br>
>><br>
>> --<br>
>> ========================================<br>
>><br>
>> Justin A. Lemkul<br>
>> Ph.D. Candidate<br>
>> ICTAS Doctoral Scholar<br>
>> MILES-IGERT Trainee<br>
>> Department of Biochemistry<br>
>> Virginia Tech<br>
>> Blacksburg, VA<br>
>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>><br>
>> ========================================<br>
>> --<br>
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><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Mon, 11 Apr 2011 14:01:58 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] How to install GROMACS in Rocks Cluster 4.5.4<br>
: ERROR<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DA34216.9050702@vt.edu">4DA34216.9050702@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Miguel Quiliano Meza wrote:<br>
> Dear community.<br>
><br>
> I have been trying to install gromacs 4.5.4 in my rocks cluster version<br>
> 5.4 but unfortunately the system showed "configure: error: Cannot find<br>
> fftw3 library" after launch the ./configure (you can see below)<br>
><br>
> Really I do not understand because I did before this:<br>
><br>
> # export LDFLAGS="-L/opt/rocks/lib"<br>
> # export CPPFLAGS="-I/opt/rocks/include"<br>
><br>
> # ./configure --enable-mpi --disable-float<br>
> --prefix=/share/apps/opt/gromacs<br>
><br>
> configure: error: Cannot find fftw3 library<br>
<br>
You have a precision mismatch. By using --disable-float you are trying to<br>
install Gromacs in double precision (which for most applications is not<br>
necessary and results in some performance loss). Thus, you need FFTW in double<br>
precision as well. You probably compiled FFTW in single precision, thus the<br>
libraries are named libfftw3f, not libfftw3.<br>
<br>
-Justin<br>
<br>
><br>
> I would be very grateful if someone could help me or give me advices. By<br>
> the way... I am trying to reproduce the steps posted in<br>
> <a href="http://software.intel.com/en-us/articles/compile-and-run-gromacs-453-in-icr/" target="_blank">http://software.intel.com/en-us/articles/compile-and-run-gromacs-453-in-icr/</a><br>
> for<br>
><br>
><br>
> "compile and run GROMACS 4.5.3 in the Intel(R) Cluster Ready Reference<br>
> Recipe S5520UR-ICR1.1-ROCKS5.3-CENTOS5.4-C2 v1.0"<br>
><br>
><br>
> and the option "--disable-float" is not clear for me.<br>
><br>
><br>
> Thank you in advance.<br>
><br>
> Miguel Quiliano.<br>
><br>
> P.S I attach the error<br>
><br>
><br>
> # ./configure --enable-mpi --disable-float --prefix=/share/apps/opt/gromacs<br>
> checking build system type... x86_64-unknown-linux-gnu<br>
> checking host system type... x86_64-unknown-linux-gnu<br>
> checking for a BSD-compatible install... /usr/bin/install -c<br>
> checking whether build environment is sane... yes<br>
> checking for a thread-safe mkdir -p... /bin/mkdir -p<br>
> checking for gawk... gawk<br>
> checking whether make sets $(MAKE)... yes<br>
> checking how to create a ustar tar archive... gnutar<br>
> checking for cc... cc<br>
> checking for C compiler default output file name... a.out<br>
> checking whether the C compiler works... yes<br>
> checking whether we are cross compiling... no<br>
> checking for suffix of executables...<br>
> checking for suffix of object files... o<br>
> checking whether we are using the GNU C compiler... yes<br>
> checking whether cc accepts -g... yes<br>
> checking for cc option to accept ISO C89... none needed<br>
> checking for style of include used by make... GNU<br>
> checking dependency style of cc... gcc3<br>
> checking dependency style of cc... gcc3<br>
> checking for mpxlc... no<br>
> checking for mpicc... mpicc<br>
> checking whether the MPI cc command works... yes<br>
> checking for MPI_IN_PLACE in collective operations... yes<br>
> checking for catamount... no<br>
> checking how to run the C preprocessor... mpicc -E<br>
> checking for grep that handles long lines and -e... /bin/grep<br>
> checking for egrep... /bin/grep -E<br>
> checking whether ln -s works... yes<br>
> checking whether mpicc accepts -O3... yes<br>
> checking whether mpicc accepts -msse2... yes<br>
> checking whether mpicc accepts -funroll-all-loops... yes<br>
> checking whether mpicc accepts -std=gnu99... yes<br>
> checking whether mpicc accepts -fexcess-precision=fast... no<br>
> checking whether mpicc accepts -O3 -fomit-frame-pointer<br>
> -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops<br>
> -std=gnu99... yes<br>
> checking whether byte ordering is bigendian... no<br>
> checking that size_t can hold pointers... yes<br>
> checking for SIGUSR1... yes<br>
> checking for pipes... yes<br>
> checking floating-point format... IEEE754 (little-endian byte and word<br>
> order)<br>
> checking whether ln -s works... yes<br>
> checking whether make sets $(MAKE)... (cached) yes<br>
> checking for a sed that does not truncate output... /bin/sed<br>
> checking for ld used by mpicc... /usr/bin/ld<br>
> checking if the linker (/usr/bin/ld) is GNU ld... yes<br>
> checking for /usr/bin/ld option to reload object files... -r<br>
> checking for BSD-compatible nm... /usr/bin/nm -B<br>
> checking how to recognise dependent libraries... pass_all<br>
> checking dlfcn.h usability... yes<br>
> checking dlfcn.h presence... yes<br>
> checking for dlfcn.h... yes<br>
> checking whether we are using the GNU C++ compiler... yes<br>
> checking whether mpicc accepts -g... yes<br>
> checking dependency style of mpicc... gcc3<br>
> checking how to run the C++ preprocessor... mpicc -E<br>
> checking the maximum length of command line arguments... 32768<br>
> checking command to parse /usr/bin/nm -B output from mpicc object... failed<br>
> checking for objdir... .libs<br>
> checking for ar... ar<br>
> checking for ranlib... ranlib<br>
> checking for strip... strip<br>
> checking if mpicc supports -fno-rtti -fno-exceptions... no<br>
> checking for mpicc option to produce PIC... -fPIC<br>
> checking if mpicc PIC flag -fPIC works... yes<br>
> checking if mpicc static flag -static works... no<br>
> checking if mpicc supports -c -o file.o... yes<br>
> checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports<br>
> shared libraries... yes<br>
> checking whether -lc should be explicitly linked in... no<br>
> checking dynamic linker characteristics... GNU/Linux ld.so<br>
> checking how to hardcode library paths into programs... immediate<br>
> checking whether stripping libraries is possible... yes<br>
> checking for shl_load... no<br>
> checking for shl_load in -ldld... no<br>
> checking for dlopen... yes<br>
> checking whether a program can dlopen itself... yes<br>
> checking whether a statically linked program can dlopen itself... yes<br>
> checking if libtool supports shared libraries... yes<br>
> checking whether to build shared libraries... yes<br>
> checking whether to build static libraries... yes<br>
> configure: creating libtool<br>
> appending configuration tag "CXX" to libtool<br>
> checking for ld used by mpicc... /usr/bin/ld -m elf_x86_64<br>
> checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes<br>
> checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports<br>
> shared libraries... yes<br>
> checking for mpicc option to produce PIC... -fPIC<br>
> checking if mpicc PIC flag -fPIC works... yes<br>
> checking if mpicc static flag -static works... no<br>
> checking if mpicc supports -c -o file.o... yes<br>
> checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports<br>
> shared libraries... yes<br>
> checking dynamic linker characteristics... GNU/Linux ld.so<br>
> checking how to hardcode library paths into programs... immediate<br>
> appending configuration tag "F77" to libtool<br>
> checking for special C compiler options needed for large files... no<br>
> checking for _FILE_OFFSET_BITS value needed for large files... no<br>
> checking for _LARGEFILE_SOURCE value needed for large files... no<br>
> checking for sqrt in -lm... yes<br>
> checking for fftw3.h... yes<br>
> checking for main in -lfftw3... no<br>
> configure: error: Cannot find fftw3 library<br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Mon, 11 Apr 2011 21:32:13 +0200<br>
From: Erik Marklund <<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>><br>
Subject: Re: [gmx-users] g_hbond<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DA3573D.80603@xray.bmc.uu.se">4DA3573D.80603@xray.bmc.uu.se</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Try the -contact option.<br>
<br>
Erik<br>
<br>
<br>
Nilesh Dhumal skrev 2011-04-11 17.12:<br>
> Is there any way to specify clorin and florin atoms as a receptor.<br>
><br>
> Nilesh<br>
><br>
> On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote:<br>
>> Nilesh Dhumal wrote:<br>
>><br>
>>> Hello,<br>
>>><br>
>>><br>
>>> I am trying to calculate number of hydrogen bond (O-H---CL)in my<br>
>>> system.<br>
>>><br>
>>> I use the following command<br>
>>><br>
>>><br>
>>><br>
>>> g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num<br>
>>><br>
>>><br>
>>> Output file hbnum.xvg shows zero number of hydorgen bond.<br>
>>><br>
>>><br>
>>> Can you tell me why its showing zero no.<br>
>>><br>
>>><br>
>>> A strong peak is found in rdf between H and CL at 2.0 A.<br>
>>><br>
>>><br>
>> Chlorine is not considered a receptor in g_hbond.<br>
>><br>
>><br>
>> -Justin<br>
>><br>
>><br>
>>> I am using Gromacs 4.0.7 version.<br>
>>><br>
>>><br>
>>><br>
>>><br>
>>> Nilesh<br>
>>><br>
>>><br>
>>><br>
>>><br>
>>><br>
>> --<br>
>> ========================================<br>
>><br>
>><br>
>> Justin A. Lemkul<br>
>> Ph.D. Candidate<br>
>> ICTAS Doctoral Scholar<br>
>> MILES-IGERT Trainee<br>
>> Department of Biochemistry<br>
>> Virginia Tech<br>
>> Blacksburg, VA<br>
>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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Erik Marklund, PhD student<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: +46 18 471 4537 fax: +46 18 511 755<br>
<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</a><br>
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Message: 4<br>
Date: Mon, 11 Apr 2011 16:55:16 -0400<br>
From: Fabian Casteblanco <<a href="mailto:fabian.casteblanco@gmail.com">fabian.casteblanco@gmail.com</a>><br>
Subject: [gmx-users] Pressure coupling problem<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <BANLkTikp48HDYw63W7vk8Tc=+<a href="mailto:TsjxqXPWw@mail.gmail.com">TsjxqXPWw@mail.gmail.com</a>><br>
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End of gmx-users Digest, Vol 84, Issue 90<br>
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