Re: [gmx-users] electron density
thanks mate! Igor Marques On Thu, May 26, 2011 at 6:12 PM, Justin A. Lemkul wrote: > > > Igor Marques wrote: > >> dear all, >> >> regarding the matter of electron density, can anyone clarify me on the >> output units? >> from this discussion i understand the values are presented in >> electrons/A^3 - is this correct? >> >> > No. It is electrons/nm^3. Standard units are defined in Chapter 2 of the > manual (and printed in the code, of course). > > -Justin > > best regards, >> igor >> >> >> Igor Marques >> >> Molecular Modeling Group – Univ. of Aveiro >> http://molecular-modeling.dq.ua.pt/ >> >> >> >> On Sat, Jan 1, 2011 at 9:01 PM, Jianhui Tian > jianhuit...@gmail.com>> wrote: >> >>Problem solved. >>The "2" in the text is just a typo when I sent the email. >>So actually there is no partial charge in the electrons.dat file. >> Thanks, Justin. >> >>Jianhui >> >>Date: Sat, 01 Jan 2011 13:56:45 -0500 >> >>From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> >>Subject: Re: [gmx-users] electron density >>To: Discussion list for GROMACS users ><mailto:gmx-users@gromacs.org>> >>Message-ID: <4d1f78ed.5070...@vt.edu <mailto:4d1f78ed.5070...@vt.edu>> >> >> >>Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> >> >>Jianhui Tian wrote: >> > Date: Fri, 31 Dec 2010 19:08:50 -0500 >> > From: "Justin A. Lemkul" ><mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu >> >><mailto:jalem...@vt.edu>>> >> > Subject: Re: [gmx-users] electron density >> > To: Discussion list for GROMACS users ><mailto:gmx-users@gromacs.org> >> > <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> > >> > Message-ID: <4d1e7092.7060...@vt.edu >><mailto:4d1e7092.7060...@vt.edu> <mailto:4d1e7092.7060...@vt.edu >> >><mailto:4d1e7092.7060...@vt.edu>>> >> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> > >> > >> > >> > Jianhui Tian wrote: >> >> Hi gmx users, >> >> >> >> I tried to calculate both the mass density and electron density >>for the >> >> water layer of a membrane simulation. The mass density is 1000 >>kg/m^3, >> >> however the electron density I got is smaller than about 0.33 >>e/A^3. I >> > >> >> How much smaller? >> > I got about 0.27 e/A^3. >> > >> >> am using a CHARMM force field and the CHARMM version of TIP3P >>water. Am >> >> I doing anything wrong when calculating the electron density? >>Thanks a >> > lot. >> >> >> > >> >> Possibly, but without seeing what you used for input, information >> > about your >> >> simulation, etc it's impossible to say. >> > In the electrons.dat file, I had >> > 2 >> > OW = 8.834 >> > HW1 = 0.583 >> > HW2 = 0.583 >> > And then used g_density ... -ei electrons.dat -dens electron ... >> > >> >>There are several problems. The first line of electrons.dat >>indicates there are >>only two unique atom names, but clearly you're supplying three. >> Second, this >>file is read in such that at integral number of electrons is >>detected on each >>line. So, in your case, two lines are being read, one that detects >>8 electrons, >>and another that detects zero. >> >>-Justin >> >>-- >>gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@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-requ...@gromacs.org >><mailto:gmx-users-requ...@gromacs.org>. >> >>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > > > Justin A. Lemkul >
Re: [gmx-users] electron density
Igor Marques wrote:
dear all,
regarding the matter of electron density, can anyone clarify me on the
output units?
from this discussion i understand the values are presented in
electrons/A^3 - is this correct?
No. It is electrons/nm^3. Standard units are defined in Chapter 2 of the
manual (and printed in the code, of course).
-Justin
best regards,
igor
Igor Marques
Molecular Modeling Group – Univ. of Aveiro
http://molecular-modeling.dq.ua.pt/
On Sat, Jan 1, 2011 at 9:01 PM, Jianhui Tian <mailto:jianhuit...@gmail.com>> wrote:
Problem solved.
The "2" in the text is just a typo when I sent the email.
So actually there is no partial charge in the electrons.dat file.
Thanks, Justin.
Jianhui
Date: Sat, 01 Jan 2011 13:56:45 -0500
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] electron density
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID: <4d1f78ed.5070...@vt.edu <mailto:4d1f78ed.5070...@vt.edu>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Jianhui Tian wrote:
> Date: Fri, 31 Dec 2010 19:08:50 -0500
> From: "Justin A. Lemkul" mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>>
> Subject: Re: [gmx-users] electron density
> To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>
> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
>
> Message-ID: <4d1e7092.7060...@vt.edu
<mailto:4d1e7092.7060...@vt.edu> <mailto:4d1e7092.7060...@vt.edu
<mailto:4d1e7092.7060...@vt.edu>>>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Jianhui Tian wrote:
>> Hi gmx users,
>>
>> I tried to calculate both the mass density and electron density
for the
>> water layer of a membrane simulation. The mass density is 1000
kg/m^3,
>> however the electron density I got is smaller than about 0.33
e/A^3. I
>
>> How much smaller?
> I got about 0.27 e/A^3.
>
>> am using a CHARMM force field and the CHARMM version of TIP3P
water. Am
>> I doing anything wrong when calculating the electron density?
Thanks a
> lot.
>>
>
>> Possibly, but without seeing what you used for input, information
> about your
>> simulation, etc it's impossible to say.
> In the electrons.dat file, I had
> 2
> OW = 8.834
> HW1 = 0.583
> HW2 = 0.583
> And then used g_density ... -ei electrons.dat -dens electron ...
>
There are several problems. The first line of electrons.dat
indicates there are
only two unique atom names, but clearly you're supplying three.
Second, this
file is read in such that at integral number of electrons is
detected on each
line. So, in your case, two lines are being read, one that detects
8 electrons,
and another that detects zero.
-Justin
--
gmx-users mailing listgmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
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http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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Re: [gmx-users] electron density
dear all, regarding the matter of electron density, can anyone clarify me on the output units? from this discussion i understand the values are presented in electrons/A^3 - is this correct? best regards, igor Igor Marques Molecular Modeling Group – Univ. of Aveiro http://molecular-modeling.dq.ua.pt/ On Sat, Jan 1, 2011 at 9:01 PM, Jianhui Tian wrote: > Problem solved. > The "2" in the text is just a typo when I sent the email. > So actually there is no partial charge in the electrons.dat file. > Thanks, Justin. > > Jianhui > > Date: Sat, 01 Jan 2011 13:56:45 -0500 > > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] electron density > To: Discussion list for GROMACS users > Message-ID: <4d1f78ed.5070...@vt.edu> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Jianhui Tian wrote: > > Date: Fri, 31 Dec 2010 19:08:50 -0500 > > From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> > > Subject: Re: [gmx-users] electron density > > To: Discussion list for GROMACS users > <mailto:gmx-users@gromacs.org> > > > > Message-ID: <4d1e7092.7060...@vt.edu <mailto:4d1e7092.7060...@vt.edu>> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > > > > > Jianhui Tian wrote: > >> Hi gmx users, > >> > >> I tried to calculate both the mass density and electron density for the > >> water layer of a membrane simulation. The mass density is 1000 kg/m^3, > >> however the electron density I got is smaller than about 0.33 e/A^3. I > > > >> How much smaller? > > I got about 0.27 e/A^3. > > > >> am using a CHARMM force field and the CHARMM version of TIP3P water. Am > >> I doing anything wrong when calculating the electron density? Thanks a > > lot. > >> > > > >> Possibly, but without seeing what you used for input, information > > about your > >> simulation, etc it's impossible to say. > > In the electrons.dat file, I had > > 2 > > OW = 8.834 > > HW1 = 0.583 > > HW2 = 0.583 > > And then used g_density ... -ei electrons.dat -dens electron ... > > > > There are several problems. The first line of electrons.dat indicates > there are > only two unique atom names, but clearly you're supplying three. Second, > this > file is read in such that at integral number of electrons is detected on > each > line. So, in your case, two lines are being read, one that detects 8 > electrons, > and another that detects zero. > > -Justin > > -- > gmx-users mailing listgmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] electron density
Problem solved. The "2" in the text is just a typo when I sent the email. So actually there is no partial charge in the electrons.dat file. Thanks, Justin. Jianhui Date: Sat, 01 Jan 2011 13:56:45 -0500 From: "Justin A. Lemkul" Subject: Re: [gmx-users] electron density To: Discussion list for GROMACS users Message-ID: <4d1f78ed.5070...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: > Date: Fri, 31 Dec 2010 19:08:50 -0500 > From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> > Subject: Re: [gmx-users] electron density > To: Discussion list for GROMACS users <mailto:gmx-users@gromacs.org> > > Message-ID: <4d1e7092.7060...@vt.edu <mailto:4d1e7092.7060...@vt.edu>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Jianhui Tian wrote: >> Hi gmx users, >> >> I tried to calculate both the mass density and electron density for the >> water layer of a membrane simulation. The mass density is 1000 kg/m^3, >> however the electron density I got is smaller than about 0.33 e/A^3. I > >> How much smaller? > I got about 0.27 e/A^3. > >> am using a CHARMM force field and the CHARMM version of TIP3P water. Am >> I doing anything wrong when calculating the electron density? Thanks a > lot. >> > >> Possibly, but without seeing what you used for input, information > about your >> simulation, etc it's impossible to say. > In the electrons.dat file, I had > 2 > OW = 8.834 > HW1 = 0.583 > HW2 = 0.583 > And then used g_density ... -ei electrons.dat -dens electron ... > There are several problems. The first line of electrons.dat indicates there are only two unique atom names, but clearly you're supplying three. Second, this file is read in such that at integral number of electrons is detected on each line. So, in your case, two lines are being read, one that detects 8 electrons, and another that detects zero. -Justin -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] electron density
Jianhui Tian wrote: Date: Fri, 31 Dec 2010 19:08:50 -0500 From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> Subject: Re: [gmx-users] electron density To: Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>> Message-ID: <4d1e7092.7060...@vt.edu <mailto:4d1e7092.7060...@vt.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: Hi gmx users, I tried to calculate both the mass density and electron density for the water layer of a membrane simulation. The mass density is 1000 kg/m^3, however the electron density I got is smaller than about 0.33 e/A^3. I How much smaller? I got about 0.27 e/A^3. am using a CHARMM force field and the CHARMM version of TIP3P water. Am I doing anything wrong when calculating the electron density? Thanks a lot. Possibly, but without seeing what you used for input, information about your simulation, etc it's impossible to say. In the electrons.dat file, I had 2 OW = 8.834 HW1 = 0.583 HW2 = 0.583 And then used g_density ... -ei electrons.dat -dens electron ... There are several problems. The first line of electrons.dat indicates there are only two unique atom names, but clearly you're supplying three. Second, this file is read in such that at integral number of electrons is detected on each line. So, in your case, two lines are being read, one that detects 8 electrons, and another that detects zero. -Justin -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] electron density
Date: Fri, 31 Dec 2010 19:08:50 -0500 From: "Justin A. Lemkul" Subject: Re: [gmx-users] electron density To: Discussion list for GROMACS users Message-ID: <4d1e7092.7060...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: > Hi gmx users, > > I tried to calculate both the mass density and electron density for the > water layer of a membrane simulation. The mass density is 1000 kg/m^3, > however the electron density I got is smaller than about 0.33 e/A^3. I > How much smaller? I got about 0.27 e/A^3. > am using a CHARMM force field and the CHARMM version of TIP3P water. Am > I doing anything wrong when calculating the electron density? Thanks a lot. > > Possibly, but without seeing what you used for input, information about your > simulation, etc it's impossible to say. In the electrons.dat file, I had 2 OW = 8.834 HW1 = 0.583 HW2 = 0.583 And then used g_density ... -ei electrons.dat -dens electron ... -Justin -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] electron density
Jianhui Tian wrote: Hi gmx users, I tried to calculate both the mass density and electron density for the water layer of a membrane simulation. The mass density is 1000 kg/m^3, however the electron density I got is smaller than about 0.33 e/A^3. I How much smaller? am using a CHARMM force field and the CHARMM version of TIP3P water. Am I doing anything wrong when calculating the electron density? Thanks a lot. Possibly, but without seeing what you used for input, information about your simulation, etc it's impossible to say. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] electron density
Hi gmx users, I tried to calculate both the mass density and electron density for the water layer of a membrane simulation. The mass density is 1000 kg/m^3, however the electron density I got is smaller than about 0.33 e/A^3. I am using a CHARMM force field and the CHARMM version of TIP3P water. Am I doing anything wrong when calculating the electron density? Thanks a lot. Jianhui -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Electron Density
afsaneh maleki wrote: Hi, I want to obtain electron density for solvent in z direction for bilayer. I used following options: ] g_density -f md.xtc -s md.tpr -d z -dens electron -o electrondens.xvg -ei electrons.dat -symm -n index.ndx Atomtapes in md.gro are OH,HW1,HW2 And “electrons.dat” file contains: 3 OW= 8 HW1=1 HW2=1 But I get error: Fatal error: Invalid line in datafile at line 1 What is my error? remove = sign Best wishes, Afsaneh Maleki -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Electron Density
Hi, I want to obtain electron density for solvent in z direction for bilayer. I used following options: ] g_density -f md.xtc -s md.tpr -d z -dens electron -o electrondens.xvg -ei electrons.dat -symm -n index.ndx Atomtapes in md.gro are OH,HW1,HW2 And “electrons.dat” file contains: 3 OW= 8 HW1=1 HW2=1 But I get error: Fatal error: Invalid line in datafile at line 1 What is my error? Best wishes, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Electron density over area
Hi, I know that electron density can be calculated by g_density. But I want to calculate electron density over area of the membrane so that I can analyze the fluctuation of the electron density with the area of the membrane. Could you tell me how to do it? Thanking you, Anirban ___ 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
Re: [gmx-users] electron density .dat file
Jian Dai wrote: Hello, all: I'm not sure how to make the .dat file in calculating the electron density, for example, If I have cholesterol.itp like: ; nrtype resnr residuatomcgnrcharge ; total charge 1 CH3 1CHOL C11 0 2 CB 1CHOL C2 2 0 3 CH2 1CHOL C33 0 4 CH2 1CHOL C44 0 5 CH1 1CHOL C55 0.14 ; charges adopted 6 OA 1CHOL O6 5 -0.54 ; from Retinol in 7 HO 1CHOL H 5 0.40 ; ffgmx.rtp ... shall I make electron_CHO.dat like: 29 C1 =6 C2 =6 C3 =6 C4 =6 C5 =6.14 O6 = 7.46 H = 1.4 or like: 29 C1 =6 C2 =6 C3 =6 C4 =6 C5 = 5.76 O6 = 8.54 H = 0.6 I mean, shall I add or subtract the partial charge? Thank you in advance and happy Thanksgiving. Jian What do you want to do with this? -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] electron density .dat file
Hello, all: I'm not sure how to make the .dat file in calculating the electron density, for example, If I have cholesterol.itp like: ; nrtype resnr residuatomcgnrcharge ; total charge 1 CH3 1CHOL C11 0 2 CB 1CHOL C2 2 0 3 CH2 1CHOL C33 0 4 CH2 1CHOL C44 0 5 CH1 1CHOL C55 0.14 ; charges adopted 6 OA 1CHOL O6 5 -0.54 ; from Retinol in 7 HO 1CHOL H 5 0.40 ; ffgmx.rtp ... shall I make electron_CHO.dat like: 29 C1 =6 C2 =6 C3 =6 C4 =6 C5 =6.14 O6 = 7.46 H = 1.4 or like: 29 C1 =6 C2 =6 C3 =6 C4 =6 C5 = 5.76 O6 = 8.54 H = 0.6 I mean, shall I add or subtract the partial charge? Thank you in advance and happy Thanksgiving. Jian ___ 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
