[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 23 13:28:26 CET 2009



Pawan Kumar wrote:
> Respected Sir,
> 
> Thanks for all your help, suggestions and guidance.
> I have few more queries.
> Which type of box is appropriate in editconf - cubic or triclinic ?

That depends entirely upon the dimensions of your system and what is adequate to 
accommodate the size of your embedded protein.

> I have read in one of your mails in the archives that POPE bilayer 
> contains some bad interactions. As it contains more no. of lipids (340) 
> it covers the full protein ( trimer which I am working on ) other than 
> the few loop regions. How far that bilayer can be used or is it fine to 
> use the biger bilayer of popc128a whcih I obtained by genconf ?
> 

The choice of lipid should not be based on a size convenience.  It should be 
based on a valid model system, and experimental evidence to which you can 
correlate your results, if possible.

POPE presented a terrible challenge, since during the in vacuo InflateGRO 
minimizations, the headgroups folded in on themselves to form intra-molecule 
hydrogen bonds that resulted in a collapse of the molecule.  The solution was to 
use freeze-grps in all dimensions during these minimizations, and then 
equilibrate very carefully.

-Justin

> Thanking you,
> Pawan
> 
> 
> 
> On Mon, Mar 23, 2009 at 5:36 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Pawan Kumar wrote:
> 
>         Respected Sir,
> 
>         Greetings from Pawan.
>         Thanks for your reply.
>         I used to do genbox first and then Inflategro all the time.
>         Is it possible to concatenate one file after the other using "
>         vi editor" - I mean just copying the contents of the
>         membrane.gro file at the end of protein.gro file ?
> 
> 
>     cat protein.gro membrane.gro > system.gro
> 
> 
>         Is it fine if I generate the .gro files using editconf command ?
> 
> 
>     Yes, you will have to center the protein and membrane appropriately,
>     within a box that has the same dimensions.
> 
>     -Justin
> 
>         Thanks for your kind help.
> 
>         Thanking you,
>         Pawan
> 
>         On Mon, Mar 23, 2009 at 5:02 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 
> 
>            Pawan Kumar wrote:
> 
>                Respected Sir,
> 
>                Greetings from Pawan.
>                Thanks for your mail.
>                I will tell you in detail.
>                The control lipid bilayer ( which is generated using genconf
>                -nbox 2 2 1 -dist 0 0 0 ) minimized fine with an emtol
>         value of
>                1510.
>                Then after inserting the protein with genbox the whole system
>                minimized with an emtol value of 2250.
>                Then I am trying to do position restraint mdrun where I am
>                getting errors.
>                Inflategro can be used only after inserting the protein right
>                (which I did using genbox with -vdwd option as 0.6) ?
> 
> 
>            No.  Read the documentation carefully.  You first concatenate
>         your
>            protein and membrane .gro files, then use InflateGRO on that
>         system.
>             There is no genbox involved when using InflateGRO, hence why I
>            suggested it as a (potentially) more reliable method.
> 
>            -Justin
> 
>                Thanking you,
>                Pawan
> 
> 
>                On Mon, Mar 23, 2009 at 4:39 PM, Justin A. Lemkul
>                <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>> wrote:
> 
> 
> 
>                   Pawan Kumar wrote:
> 
>                       Hello Justin Sir,
> 
>                       Greetings from Pawan.
>                       Sorry for the inconvenience.
>                       Next time I will keep in mind about the subject line.
>                       I tried deleting those particular atoms where it
>         gave the
>                       maximum force.
> 
> 
>                   You said that this atom was part of a lipid.  Deleting
>         these
>                atoms
>                   will give you a broken structure and an unrealistic
>         system.  It
>                   should also cause grompp to complain.
> 
> 
>                       But every time a new atom with a maximum force was
>         given
>                in the
>                       output.
>                       Is it fine to use to use "constraints = all-angles" in
>                order to
>                       overcome the Lincs warnings ?
> 
> 
>                   No.  LINCS warnings indicate that there is something
>                fundamentally
>                   wrong with your system.  It likely stems from how you
>                inserted your
>                   protein into the lipids.  Think about it.  Your
>         control lipid
>                   bilayer minimized fine.  Your protein-membrane system does
>                not, if
>                   that is what we're still talking about. That indicates
>         to me that
>                   the problem is not with the lipids, the problem is
>         with the
>                   insertion of the protein.
> 
>                   Instead of genbox (which is somewhat crude), try the
>         InflateGRO
>                   script from Tieleman's site.  I have used it many
>         times to build
>                   nicely-packed membrane protein systems.  It takes
>         substantially
>                   longer to build the system than with genbox, but I
>         think the
>                results
>                   are more reliable.
> 
>                   -Justin
> 
>                       Thanks in advance.
> 
>                       Thanking you,
>                       Pawan
> 
> 
> 
> 
>                       On Mon, Mar 23, 2009 at 4:16 PM, Justin A. Lemkul
>                       <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
>                       <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>> wrote:
> 
> 
>                          When replying to digests, please change the subject
>                line to
>                          something relevant.
> 
>                          Pawan Kumar wrote:
> 
>                              Hello Justin Sir,
> 
>                              Greetings from Pawan.
>                              Sorry for the late reply.
>                              The max. force was 1.2447973e+o5 on atom 19448.
> 
> 
>                          An Fmax that high is sure to generate problems.
>          It is
>                up to
>                       you to
>                          inspect your system, understand which atoms are
>                interacting
>                       to cause
>                          such a force, and determine if you've done
>         something
>                wrong.
> 
>                          -Justin
> 
>                              This particular atom belongs to one of the
>         lipid
>                residues
>                       of the
>                              bilayer.
>                              I get Lincs warnings whenever I run the
>         position
>                       restraint mdrun.
> 
>                              Thanking you,
>                              Pawan
> 
> 
>                              On Sat, Mar 21, 2009 at 6:08 PM, Justin A.
>         Lemkul
>                              <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
>                       <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>
>                              <mailto:jalemkul at vt.edu
>         <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>         <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
>                       <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>>> wrote:
> 
> 
> 
>                                 Pawan Kumar wrote:
> 
>                                     Hello Justin Sir,
> 
>                                     Greetings from Pawan
>                                     Thanks for your valuable suggestion
>         and reply.
>                                     Initially I gave the emtol of 1000
>         and the
>                output
>                       I got was :
>                                     Steepest Descents converged to machine
>                precision
>                       in 163 steps
>                                     but did not reach the requested
>         Fmax<1000.
>                                     Potential Energy = - 4.4516497e+05
> 
> 
>                                 ...and how close did Fmax get to 1000?
> 
> 
>                                     Even I tried to minimize the popc
>         bilayer
>                which I
>                       took from
>                                     Tieleman sir's website ( before
>         generating a
>                       bigger bilayer
>                                     using genconf ) but that also
>         converged to
>                machine
>                              precision but
>                                     not to the requested Fmax<1000. How do I
>                proceed
>                       further ?
> 
> 
>                                 Well, these things are not absolute;
>         Fmax = 1000 is
>                       kind of a
>                              rule
>                                 of thumb that I use in my own work, but
>                sometimes it
>                       is not
>                                 necessary.  Careful equilibration should
>                massage your
>                       system into
>                                 cooperating.
> 
>                                 -Justin
> 
>                                     Thanks for your suggestions and help.
> 
>                                     Thanking you,
>                                     Pawan
> 
>                                     On Thu, Mar 19, 2009 at 9:13 PM,
> 
>                                        Pawan Kumar wrote:
>                                         > Hello Justin Sir,
>                                         >
>                                         > Greetings from Pawan
>                                         > Thanks for your valuable
>         suggestion
>                and reply.
>                                         > After inserting the protein in the
>                bilayer using
>                              genbox I have
>                                        minimized
>                                         > the whole system without using any
>                position
>                       restraints
>                                     (i.e. define =
>                                         > -DFLEXIBLE in em.mdp file). I used
>                vanderwaal's
>                              distance
>                                     parameter (
>                                         > -vdwd of 0.6 ) in the genbox step.
>                                         > After running mdrun for energy
>                minimization
>                       I got the
>                                     output as :
>                                         > Steepest Descents converged to
>                Fmax<2250 in
>                       14 steps.
>                                         > Potential energy = - 6.9484700e+05
>                                         > Maximum force = 2.2114819e+03
>         on atom
>                34277
>                                         > Norm. of force = 5.0103039e+04
>                                         >
> 
>                                        You should try for an Fmax of no
>         greater
>                than 1000.
>                               2250 is
>                                     still
>                                        very high.
> 
>                                         > I tried decreasing the emtol
>         value in
>                the em.mdp
>                              file but it
>                                        ended with
>                                         > machine precision.
> 
>                                        How far did it converge?  What
>         was Fmax?
> 
>                                         > I have read in literature that
>         5000
>                steps of
>                       Steetest
>                                     Descents run is
>                                         > required after inserting the
>         protein
>                in the
>                       bilayer
>                              which
>                                     should be
>                                         > followed by atleast 1000 steps of
>                conjugate
>                              gradients. How
>                                     can I
>                                         > accomplish this ? Is there any
>                parameter to be
>                              given in the
>                                        em.mdp file
>                                         > ? I use steep as the integrator in
>                the mdp
>                       file for
>                              energy
>                                        minimization.
> 
>                                        Read the manual.
> 
>                                        Whether or not that exact setup
>         is going
>                to be
>                              "required" is
>                                     likely
>                                        system-specific.  I would say that as
>                long as
>                       your system
>                                     converges
>                                        to a stable,
>                                        negative Epot with a reasonable Fmax
>                (less than
>                       1000,
>                              but ideally
>                                        lower) then
>                                        you *may* have an appropriate
>         starting
>                structure.
> 
>                                        -Justin
> 
>                                         > Please help with some suggestions.
>                                         > Thanks in advance.
>                                         >
>                                         > Thanking you,
>                                         > Pawan
>                                         >
>                                         >
>                                         >
> 
> 
> 
>                                                      
>         ------------------------------------------------------------------------
> 
>                                    
>         _______________________________________________
>                                     gmx-users mailing list          
>         gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>         <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>                       <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>>>
>                              <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>> <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>>>>
>                                     <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>                       <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>>> <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>                       <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at 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
>                       gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>>
>                              <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>
>                       <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>>>
>                                    
>         <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>
>                       <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>>
>                              <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>
>                       <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>>>>.
>                                     Can't post? Read
>                              http://www.gromacs.org/mailing_lists/users.php
> 
> 
>                                 --  
>          ========================================
> 
>                                 Justin A. Lemkul
>                                 Graduate Research Assistant
>                                 ICTAS Doctoral Scholar
>                                 Department of Biochemistry
>                                 Virginia Tech
>                                 Blacksburg, VA
>                                 jalemkul[at]vt.edu <http://vt.edu>
>         <http://vt.edu>
>                <http://vt.edu> <http://vt.edu>
>                       <http://vt.edu> | (540)
> 
>                              231-9080
>                                      
>         http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>                                 ========================================
>                                
>         _______________________________________________
>                                 gmx-users mailing list  
>          gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>                       <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>>>
>                              <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>> <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>>>>
>                                 <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>                       <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>>> <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>                       <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at 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
>                gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>         <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>
>                       <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>>
>                              <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>
>                       <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>>>
>                                 <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>
>                       <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>>
>                              <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>
>                       <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>>>>.
>                                 Can't post? Read
>                       http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
>                          --    ========================================
> 
>                          Justin A. Lemkul
>                          Graduate Research Assistant
>                          ICTAS Doctoral Scholar
>                          Department of Biochemistry
>                          Virginia Tech
>                          Blacksburg, VA
>                          jalemkul[at]vt.edu <http://vt.edu>
>         <http://vt.edu> <http://vt.edu>
>                <http://vt.edu> | (540)
>                       231-9080
>                        
>          http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>                          ========================================
>                          _______________________________________________
>                          gmx-users mailing list    gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>                       <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>>>
>                          <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>> <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at 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
>         gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>
>                       <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>>
>                          <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>
>                       <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>>>.
>                          Can't post? Read
>                http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
>                   --    ========================================
> 
>                   Justin A. Lemkul
>                   Graduate Research Assistant
>                   ICTAS Doctoral Scholar
>                   Department of Biochemistry
>                   Virginia Tech
>                   Blacksburg, VA
>                   jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu>
>         <http://vt.edu> | (540)
>                231-9080
>                   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>                   ========================================
> 
> 
> 
>            --    ========================================
> 
>            Justin A. Lemkul
>            Graduate Research Assistant
>            ICTAS Doctoral Scholar
>            Department of Biochemistry
>            Virginia Tech
>            Blacksburg, VA
>            jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>         231-9080
>            http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>            ========================================
>            _______________________________________________
>            gmx-users mailing list    gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>            <mailto:gmx-users at gromacs.org <mailto:gmx-users at 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 gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>            <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>.
> 
>            Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     ICTAS Doctoral Scholar
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
>     _______________________________________________
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at 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 gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



More information about the gromacs.org_gmx-users mailing list