Dear Mark,<div><br></div><div>Thanks a lot for the reply and highlighting the cause of error that I was facing.</div><div>Still can it be possible to overcome the same error with the available facility.</div><div><br></div>
<div> Pavan Payghan</div><div>
<div> </div>
<div> </div>
<div> </div><br>
<br><br><div class="gmail_quote">On Thu, Apr 26, 2012 at 9:55 AM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<br>
Today's Topics:<br>
<br>
1. Free Energy calcualtions (Sai Kumar Ramadugu)<br>
2. How to choose two atoms at the same time, using g_select<br>
selection.dat (mu xiaojia)<br>
3. Re: How to choose two atoms at the same time, using g_select<br>
selection.dat (Justin A. Lemkul)<br>
4. Re: why it is so slow in Blue gene? (Mark Abraham)<br>
5. Fwd: Error: coordinate file does not match with the topology<br>
file (Mark Abraham)<br>
6. Re: How to increase the ratio of cell size to constrain<br>
length per error message (Mark Abraham)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 25 Apr 2012 16:05:05 -0500<br>
From: Sai Kumar Ramadugu <<a href="mailto:sramadugu@gmail.com" target="_blank">sramadugu@gmail.com</a>><br>
Subject: [gmx-users] Free Energy calcualtions<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:CAO6uzQUPcXNcot6qbkWLrrrifpk2Y3ciCfFTs7%2BFwYyJrb0smg@mail.gmail.com" target="_blank">CAO6uzQUPcXNcot6qbkWLrrrifpk2Y3ciCfFTs7+FwYyJrb0smg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi Gromacs Users,<br>
I want to mutate a glutamate in my protein to alanine in presence of a<br>
ligand.<br>
With glutamate, the protein charge is -3. To neutralize the system, I added<br>
3K+ ions.<br>
Now when I mutate GLU to ALA, the charge in state_B will be +1 (protein -2<br>
+ 3K+).<br>
<br>
Right now I'm in the charge part of the mutation. Once this is successful,<br>
I will include the VDW mutation too.<br>
<br>
I have added the mutation details of Glu to Ala residue in the topology in<br>
[atoms], [bonds], [angles] and [dihedrals] sections.<br>
<br>
After I run the grompp command, the result says that my State_B topology<br>
has +1 charge since I am not including mutation of one K+ ion to neutral K+<br>
ion.<br>
How can I mutate 1 particular K+ to K atom and subsequently to a dummy<br>
atom? Since I'm using OPLS force field, we have ions.itp to be used in the<br>
topology file, changing one K+ is making it troublesome for me to implement<br>
in the topology file.<br>
Any suggestions are helpful.<br>
<br>
Thanks for your time.<br>
<br>
Regards<br>
Sai<br>
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Message: 2<br>
Date: Wed, 25 Apr 2012 20:19:22 -0500<br>
From: mu xiaojia <<a href="mailto:muxiaojia2010@gmail.com" target="_blank">muxiaojia2010@gmail.com</a>><br>
Subject: [gmx-users] How to choose two atoms at the same time, using<br>
g_select selection.dat<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:CABSFTFqreE885zmhdQq6n2qrjcKo2c-SdupOT_utJbXKKyoqLw@mail.gmail.com" target="_blank">CABSFTFqreE885zmhdQq6n2qrjcKo2c-SdupOT_utJbXKKyoqLw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear gmx users,<br>
<br>
I may have a silly question, how to make a group of two atoms from the same<br>
molecule?<br>
<br>
e.g, I want to make an "HN" group of both H and N from my 2nd residue,<br>
<br>
I know for single one, commands in *.dat file is like:<br>
<br>
nameN = resnr 2 and name N;<br>
nameH = resnr 2 and name H;<br>
<br>
nameN;<br>
nameH;<br>
<br>
I guess "merge" or "plus" might be helpful,I think it should be done<br>
something like: "nameN_H = resnr 2 and name N ?? resnr 2 and name H", so it<br>
is an intramolecular combination between N and H; it shouldn't be done<br>
afterwards, otherwise it would be an intermolecular combination.<br>
<br>
Thanks very much! g_select is really powerful, and hopefully there would be<br>
more examples.<br>
<br>
Jia<br>
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<br>
Message: 3<br>
Date: Wed, 25 Apr 2012 21:24:21 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] How to choose two atoms at the same time,<br>
using g_select selection.dat<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4F98A3C5.8040904@vt.edu" target="_blank">4F98A3C5.8040904@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
On 4/25/12 9:19 PM, mu xiaojia wrote:<br>
> Dear gmx users,<br>
><br>
> I may have a silly question, how to make a group of two atoms from the same<br>
> molecule?<br>
><br>
> e.g, I want to make an "HN" group of both H and N from my 2nd residue,<br>
><br>
> I know for single one, commands in *.dat file is like:<br>
><br>
> nameN = resnr 2 and name N;<br>
> nameH = resnr 2 and name H;<br>
><br>
> nameN;<br>
> nameH;<br>
><br>
> I guess "merge" or "plus" might be helpful,I think it should be done something<br>
> like: "nameN_H = resnr 2 and name N ?? resnr 2 and name H", so it is an<br>
> intramolecular combination between N and H; it shouldn't be done afterwards,<br>
> otherwise it would be an intermolecular combination.<br>
><br>
> Thanks very much! g_select is really powerful, and hopefully there would be more<br>
> examples.<br>
><br>
<br>
g_select is more suited for complex groups that are dynamic or otherwise based<br>
on geometric criteria. If you're trying to make a simple group that consists of<br>
2 atoms, make_ndx is easier, and using a plain text editor will be easiest, i.e.:<br>
<br>
[ my_group ]<br>
1 2<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>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Thu, 26 Apr 2012 14:04:49 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] why it is so slow in Blue gene?<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4F98C961.9030105@anu.edu.au" target="_blank">4F98C961.9030105@anu.edu.au</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
On 25/04/2012 3:24 PM, Albert wrote:<br>
> hello:<br>
><br>
> it is blue gene P. And the gromacs is single precision in the<br>
> cluster. Getting Loaded...And the administrator told me that I have to<br>
> use the multiples of 32 in the bg_size parameter. The number specified<br>
> in "-np" should be 4 times bg_size.<br>
<br>
Yes, but your system is too small to make use of 128 processors. Also,<br>
get rid of -launch and -nt from your command line, since they do nothing.<br>
<br>
> It is even slower than my own workstation with 16 core.........<br>
><br>
><br>
><br>
><br>
> here is the log file I get:<br>
<br>
No, that's the stdout file. Look at the end of the .log file.<br>
<br>
><br>
> -------------log----------------<br>
> Reading file npt_01.tpr, VERSION 4.5.5 (single precision)<br>
> Loaded with Money<br>
><br>
> Will use 112 particle-particle and 16 PME only nodes<br>
<br>
This is guaranteed to lead to woeful performance with your .mdp<br>
settings, but you will have to look towards the beginning of the .log<br>
file to find out why mdrun selected this. Odds are good that your system<br>
size is so small that the minimum particle-particle cell size<br>
(constrained by rcoulomb) doesn't give mdrun any good options that use<br>
all the processors. You'd likely get better raw performance with twice<br>
the number of atoms or half the number of processors.<br>
<br>
Mark<br>
<br>
> This is a guess, check the performance at the end of the log file<br>
> Making 3D domain decomposition 4 x 4 x 7<br>
> starting mdrun 'GRowing Old MAkes el Chrono Sweat'<br>
> 500000 steps, 500.0 ps.<br>
> step 0<br>
> vol 0.64! imb F 16% pme/F 0.22 step 100, will finish Wed Apr 25<br>
> 18:28:06 2012<br>
> vol 0.65! imb F 17% pme/F 0.21 step 200, will finish Wed Apr 25<br>
> 18:09:54 2012<br>
> vol 0.67! imb F 18% pme/F 0.21 step 300, will finish Wed Apr 25<br>
> 18:03:12 2012<br>
> vol 0.69! imb F 18% pme/F 0.21 step 400, will finish Wed Apr 25<br>
> 17:58:25 2012<br>
> vol 0.67! imb F 19% pme/F 0.21 step 500, will finish Wed Apr 25<br>
> 17:55:26 2012<br>
> vol 0.68! imb F 19% pme/F 0.22 step 600, will finish Wed Apr 25<br>
> 17:53:31 2012<br>
> vol 0.68! imb F 19% pme/F 0.22 step 700, will finish Wed Apr 25<br>
> 17:51:57 2012<br>
> vol 0.68! imb F 19% pme/F 0.22 step 800, will finish Wed Apr 25<br>
> 17:50:32 2012<br>
> vol 0.68! imb F 20% pme/F 0.22 step 900, will finish Wed Apr 25<br>
> 17:49:14 2012<br>
> vol 0.67! imb F 21% pme/F 0.22 step 1000, will finish Wed Apr 25<br>
> 17:48:13 2012<br>
> vol 0.68! imb F 20% pme/F 0.22 step 1100, will finish Wed Apr 25<br>
> 17:47:28 2012<br>
> vol 0.67! imb F 21% pme/F 0.22 step 1200, will finish Wed Apr 25<br>
> 17:46:50 2012<br>
> vol 0.67! imb F 21% pme/F 0.22 step 1300, will finish Wed Apr 25<br>
> 17:46:15 2012<br>
><br>
><br>
><br>
> On 04/24/2012 06:01 PM, Hannes Loeffler wrote:<br>
>> On Tue, 24 Apr 2012 15:42:15 +0200<br>
>> Albert<<a href="mailto:mailmd2011@gmail.com" target="_blank">mailmd2011@gmail.com</a>> wrote:<br>
>><br>
>>> hello:<br>
>>><br>
>>> I am running a 60,000 atom system with 128 core in a blue gene<br>
>>> cluster. and it is only 1ns/day.... here is the script I used for<br>
>> You don't give any information what exact system that is (L/P/Q?), if<br>
>> you run single or double precision and what force field you are using.<br>
>> But for a similar sized system using a united atom force field in<br>
>> single precision we find about 4 ns/day on a BlueGene/P (see our<br>
>> benchmarking reports on<br>
>> <a href="http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx" target="_blank">http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx</a>). I would<br>
>> expect a run with the CHARMM 27 force field in double precision to be<br>
>> roughly 3 times slower. We found scaling to 128 cores to be<br>
>> reasonably good. Also, check our report for problems when compiling<br>
>> with higher optimisation.<br>
>><br>
>> Hannes.<br>
><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Thu, 26 Apr 2012 14:13:06 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
Subject: [gmx-users] Fwd: Error: coordinate file does not match with<br>
the topology file<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4F98CB52.1060606@anu.edu.au" target="_blank">4F98CB52.1060606@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Please do not make unsolicited general GROMACS inquiries to private<br>
email addresses. The mailing lists exist for these kinds of purposes.<br>
<br>
On point, you cannot be helped unless you provide the command lines that<br>
you used and describe the objectives you were trying to achieve.<br>
Whatever changes you make to one of the coordinate and .top file must be<br>
matched in the other.<br>
<br>
Mark<br>
<br>
-------- Original Message --------<br>
Subject: Error: coordinate file does not match with the topology file<br>
Date: Wed, 25 Apr 2012 02:05:45 +0800 (SGT)<br>
From: sonali shinde <<a href="mailto:shindesonali14@yahoo.co.in" target="_blank">shindesonali14@yahoo.co.in</a>><br>
Reply-To: sonali shinde <<a href="mailto:shindesonali14@yahoo.co.in" target="_blank">shindesonali14@yahoo.co.in</a>><br>
To: <a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>><br>
<br>
<br>
<br>
<br>
----- Forwarded Message -----<br>
*From:* sonali shinde <<a href="mailto:shindesonali14@yahoo.co.in" target="_blank">shindesonali14@yahoo.co.in</a>><br>
*To:* vini k <<a href="mailto:vineetha_mandlik@yahoo.co.in" target="_blank">vineetha_mandlik@yahoo.co.in</a>><br>
*Sent:* Monday, 23 April 2012 6:48 PM<br>
*Subject:* Error: coordinate file does not match with the topology file<br>
<br>
Dear Sir,<br>
I am a user of gromacs 4.0 for molecular dynamic study of<br>
a protein molecule. I have generated trajectory file before using the<br>
same commands that I use now. Recently I am suffering some problem using<br>
Gromacs , my coordinate file does not matches with the topology file.I<br>
have attached the pdb file protein, .gro and .top file . I have<br>
encountered same error a number of times with three different<br>
proteins.Please suggest the answer for the same.<br>
Thanking you.<br>
<br>
<br>
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<br>
Message: 6<br>
Date: Thu, 26 Apr 2012 14:24:53 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] How to increase the ratio of cell size to<br>
constrain length per error message<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4F98CE15.4040309@anu.edu.au" target="_blank">4F98CE15.4040309@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 25/04/2012 6:28 AM, PAVAN PAYGHAN wrote:<br>
><br>
> Dear Gromacs Users,<br>
><br>
> I am using gromacs version is 4.5.3.and running my jobs on single node<br>
> with 8 cores.<br>
><br>
> I have two different systems which contain about 425000 atoms (protein<br>
> + Lipid +SOL) one with bound ligand<br>
><br>
> and another one unbound protein.I have successfully reached up to<br>
> NPT equilibration run step,<br>
><br>
<br>
It is a poor idea to do equilibration with Parinello-Rahman, which is<br>
unstable when the system is not already close to equilibrium. For some<br>
reason people still do it, despite at least a post per week on this list<br>
suggesting against it, and a warning in the manual. Use Berendsen to fix<br>
the density, then equilibrate further with P-R to get the right ensemble.<br>
<br>
> now I want to continue the same for production run. Without ligand I<br>
> am able to run successfully But the same system with ligand is<br>
> crashing with following error-<br>
><br>
> D D cell 1 0 0 could only obtain 1520 of the 1521 atoms that are<br>
><br>
> are connected via constraints from the neighbouring cells<br>
><br>
> This probably means your constraint length are too long<br>
><br>
> compared to the domain decomposition cell size.<br>
><br>
> Decrease the number of domain decomposition grid cells or lincs_order.<br>
><br>
<br>
I'd rather expect your system was blowing up because of the above issue.<br>
Perhaps the suggestion in the error message is not as complete as could<br>
be desired - you have so many atoms per processor that the constraint<br>
length would normally be tiny with respect to the cell size. So I think<br>
the things you have tried below are rearranging the deck chairs on the<br>
Titanic.<br>
<br>
Mark<br>
<br>
> Accordingly following the suggestions given in the error I tried to<br>
> solve it with<br>
><br>
> Following log file and changed,<br>
><br>
> 1.1. -rcon<br>
><br>
> Estimated maximum distance required for p-lincs was 0.877 thus<br>
> I increased it to 0.900<br>
><br>
> then it thrown another error.<br>
><br>
> The initial cell size (0.877) is smaller than the cell size limit<br>
> (0.900)<br>
><br>
><br>
> 2 .Then I tried to increase the --dds and --rdd from original values<br>
> of 1.25 and 0.623 to 1.30 and 0.670 respectively.<br>
><br>
> But it does not help and ended with run crash.<br>
><br>
> /*What I did was logical or I did it wrongly?*/<br>
><br>
> /*Now can anyone please suggest me the appropriate way to deal with<br>
> the problem mentioned above? */<br>
><br>
> As I want the continuation of the same run without altering the output<br>
> after change in the parameters (As I have to compare the output with<br>
> unbound protein run thus can't afford change in output with change in<br>
> parameters)<br>
><br>
> I know that I need to change some of the parameters in .mdp file such as<br>
><br>
> fourierspacing from 0.16 to 0.12 and on the contrary increase the<br>
> pme_order from say 4 to 6.<br>
><br>
> /*But as asked above by doing so the output will not or will be the<br>
> exact continuation run?*/<br>
><br>
> /*How to increase the ratio of cell size to constrain length per error<br>
> message?*/<br>
><br>
> /*If any better way of doing so without changing the output please<br>
> suggest,*/<br>
><br>
> I am suffering from the same problem since long,<br>
><br>
> Please help me .Please see the mdp file for the reference.<br>
><br>
> integrator = md<br>
><br>
> nsteps = 10000000<br>
><br>
> dt = 0.002 ; 2 fs<br>
> > ><br>
> ; Output control<br>
> nstxout = 1000 ;<br>
> nstvout = 1000 ;<br>
> nstxtcout = 1000 ;<br>
><br>
> nstenergy = 1000 ;<br>
><br>
> nstlog = 1000 ;<br>
> ; Bond parameters<br>
> continuation = yes ; Restarting after NPT<br>
> constraint_algorithm = lincs ; holonomic constraints<br>
> constraints = all-bonds ; all bonds (even heavy atom-H<br>
> bonds)<br>
> lincs_iter = 1 ; accuracy of LINCS<br>
> lincs_order = 4<br>
><br>
> ; Neighborsearching<br>
> ns_type = grid<br>
> nstlist = 5<br>
><br>
> rlist = 1.2<br>
> rcoulomb = 1.2<br>
> rvdw = 1.2<br>
> ; Electrostatics<br>
> coulombtype = PME<br>
> pme_order = 4<br>
> fourierspacing = 0.16<br>
> tcoupl = Nose-Hoover<br>
> tc-grps = Protein P SOL_NA_CL ;<br>
> tau_t = 0.5 0.5 0.5<br>
> ref_t = 323 323 323 group, in K<br>
> ; Pressure coupling is on<br>
> pcoupl = Parrinello-Rahman ;<br>
><br>
> pcoupltype = semiisotropic<br>
> tau_p = 2.0 ; time<br>
> ref_p = 1.0 1.0 ; reference<br>
> compressibility = 4.5e-5 4.5e-5 ;<br>
><br>
> ; Periodic boundary conditions<br>
> pbc = xyz ; 3-D PBC<br>
><br>
> ; Dispersion correction<br>
> DispCorr = EnerPres ; account for cut-off vdW scheme<br>
><br>
> ; Velocity generation<br>
> gen_vel = no<br>
><br>
> Thanking in Advance<br>
><br>
><br>
><br>
<br>
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End of gmx-users Digest, Vol 96, Issue 189<br>
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