<br><br><div class="gmail_quote">On Thu, Apr 23, 2009 at 11:55 AM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. Re: np command with GROMACS 4.0.4 (Vitaly V. Chaban)<br>
2. Re: RMSD of Aminoacids (Mark Abraham)<br>
3. problem in topology file of protein-lipid bilayer system for<br>
grompp (nitu sharma)<br>
4. validating gromacs installation 4.0.4 ( Y. U. Sasidhar )<br>
5. Re: problem in topology file of protein-lipid bilayer system<br>
for grompp (Mark Abraham)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 22 Apr 2009 22:36:51 +0200<br>
From: "Vitaly V. Chaban" <<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>><br>
Subject: [gmx-users] Re: np command with GROMACS 4.0.4<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:7138ee40904221336u626133d5mdcf42f1b47e70acd@mail.gmail.com">7138ee40904221336u626133d5mdcf42f1b47e70acd@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
If seems in the gmx versions above 4.0 '-np' is not used. If I am not<br>
mistaken you should just point out the number of nodes in your queueing<br>
system while submitting the job.<br>
<br>
Vitaly<br>
<br>
<br>
> I am trying to do my position restrained dynamic simulation on GROMACS<br>
> 4.0.4, and I want to use 4 nodes on the cpu cluster available at my campus;<br>
> I typed in the following grompp command:<br>
><br>
> grompp -np 4 -f pr.mdp -c BR6_em.pdb -p BR6.top -o BR6_pr.tpr -n prot.ndx<br>
> -maxwarn 10<br>
><br>
> and it gave me the response that -np is an invalid command.<br>
><br>
> How do I get grompp to rec. that I want to use 4 processors? Because my<br>
> job<br>
> script where I have specified 4 nodes, will not work unless I have np 4<br>
> included in my grompp. I did see that it works with GROMACS 3.3.3...but is<br>
> there a way to do it with 4.0.4?<br>
><br>
> Thanks so much!<br>
><br>
> Halie Shah<br>
> University of Houston, TX U.S.<br>
> Briggs Lab<br>
><br>
><br>
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Message: 2<br>
Date: Thu, 23 Apr 2009 10:04:36 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] RMSD of Aminoacids<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:49EFB094.9040908@anu.edu.au">49EFB094.9040908@anu.edu.au</a>><br>
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<br>
Andy Torres wrote:<br>
> Hi, I'm trying to compare two proteins with the same number of<br>
> aminoacids with g_confrms, and it works all right, but it gives me the<br>
> RMSD of the hole protein, and I need the distances (or deviations) of<br>
> each aminoacid. I know this data shoul be there, but I don't know how to<br>
> get it (I've got the mean structure of each protein, calculated with<br>
> g_rmsf, but this data is not fitted each other)<br>
<br>
Have a look at g_confrms -h. Probably with the right index groups<br>
constructed you can fit with one group and observe the RMSD with another.<br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 23 Apr 2009 10:31:10 +0530<br>
From: nitu sharma <<a href="mailto:sharmanitu35@gmail.com">sharmanitu35@gmail.com</a>><br>
Subject: [gmx-users] problem in topology file of protein-lipid bilayer<br>
system for grompp<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:5fe39aa90904222201n7e5181c4p87111ffd86958741@mail.gmail.com">5fe39aa90904222201n7e5181c4p87111ffd86958741@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear Justin<br>
<br>
I am doing simulation of membrane protein .I<br>
follow your tutorial for that I think its perfect for that. But I am getting<br>
problem in doing inflategro step, I alredy discuss this problem with you but<br>
now I am starting everything fresh I have completed upto concatanation of<br>
protein with lipid bilayer after that for packing of lipid around protein I<br>
am using inflategro script from teleman website . Problem came in second<br>
step of inflategro i.e for energy minimisation for this I need topology file<br>
of "protein-lipid system".<br>
I am giving you information in detail i.e -<br>
for topology file I have made changes in topol.top file which I got from<br>
pdb2gmx command in first step for protein processing ,the topol .top file is<br>
like this-<br>
File 'topol.top' was generated<br>
; By user: nitu (504)<br>
; On host: localhost.localdomain<br>
; At date: Thu Apr 16 23:20:48 2009<br>
;<br>
; This is your topology file<br>
; Grunge ROck MAChoS<br>
;<br>
; Include forcefield parameters<br>
#include "ffG53a6.itp"<br>
<br>
; Include chain topologies<br>
#include "topol_A.itp"<br>
#include "topol_B.itp"<br>
<br>
; Include water topology<br>
#include "spc.itp"<br>
<br>
#ifdef POSRES_WATER<br>
; Position restraint for each water oxygen<br>
[ position_restraints ]<br>
; i funct fcx fcy fcz<br>
1 1 1000 1000 1000<br>
#endif<br>
<br>
; Include generic topology for ions<br>
#include "ions.itp"<br>
<br>
[ system ]<br>
; Name<br>
Grunge ROck MAChoS<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
Protein_A 1<br>
Protein_B 1<br>
**********<br>
And the change topology file is like this-<br>
<br>
; Include forcefield parameters<br>
#include "ffG53a6_lipid.itp"<br>
<br>
; Include chain topologies<br>
#include "topol_A.itp"<br>
#include "topol_B.itp"<br>
<br>
#ifdef POSRES<br>
#include "posre_A.itp"<br>
#include "posre_B.itp"<br>
#endif<br>
<br>
; Include DMPC chain topology<br>
#include "dmpc.itp"<br>
<br>
<br>
[ system ]<br>
; Name<br>
Protein in DMPC bilayer<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
Protein_A 1<br>
Protein_B 1<br>
DMPC 128<br>
<br>
but when I gave this topology file to grompp it shws error-<br>
no. of coordinates in coordinate file doesn,t mach the topology file .<br>
<br>
Can you suggest me something for making topology file for protein-lipid<br>
bilayer system. Is there any other method for making topology file ,I have<br>
read in mannual chapter 5 but there is also mentioned same method.<br>
If possible please help me becoz without solving this problem I can't move<br>
for furthur processing .<br>
<br>
* My gro file of protein shows 9902 atoms .<br>
As you ask in previous mail is .itp file have [ molecules ] section the<br>
answer is the .itp file haven't molecules section it have [molecule type ]<br>
section can it also create problem for topology file working.<br>
<br>
Thanks a lot justin .<br>
I am waiting for your reply.<br>
<br>
Nitu sharma<br>
School of life sciences<br>
Jawaherlal Nehru University<br>
New delhi , India<br>
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<br>
Message: 4<br>
Date: Thu, 23 Apr 2009 10:53:13 +0530<br>
From: " Y. U. Sasidhar " <<a href="mailto:sasidhar@chem.iitb.ac.in">sasidhar@chem.iitb.ac.in</a>><br>
Subject: [gmx-users] validating gromacs installation 4.0.4<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:49EFFB41.3060204@chem.iitb.ac.in">49EFFB41.3060204@chem.iitb.ac.in</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Dear Users, I posted the following message a few days ago; So far I have<br>
not got any response. Searching archives also seem to indicate that<br>
people are facing similar problems. Some times modifying mdp options<br>
make the tests "pass" as we also observed ( see below ).<br>
<br>
Further the reference trajectories seem to be generated by versions<br>
3.2/3.3.<br>
<br>
Are there reference trajectories for 4.0.4?<br>
<br>
If some of the tests "fail", does it mean gromacs is not computing as it<br>
should? the results can not be relied on?<br>
<br>
As of now numbers are compared to test pass/failure.<br>
<br>
Can physical properties - like rdf of spc water, diffusion constants<br>
etc- be used to test gromacs?<br>
<br>
I thank you very much for your time.<br>
<br>
The "failures" are presenting a dilemma. I hope I have done what I can<br>
as a user and hope to resolve the issue with your help.<br>
<br>
regards,<br>
<br>
Sasidhar<br>
<br>
PS: we notice that with double precision failures are less; further with<br>
version 3.2 the failures are less suggesting that numerical accuracies<br>
of machines, differences in algorithms, if any, used in different<br>
versions could be a cause for "failures"<br>
==============previously posted message=============<br>
<br>
<br>
<br>
Dear users,<br>
<br>
We have installed gmx 4.0.4 ( single precision, on cent os 4.3 ( 32 bit<br>
) on quad core dual xeon machine ( clock 2 GHz )<br>
<br>
Installation directions as given on the site followed.<br>
And the tests are run using the perl script provided plus test<br>
files/folders.<br>
<br>
We find many failures ( see below ); However, by changing mdp options<br>
all the tests "passed" as detailed below. For example, for the "field"<br>
test coulomb type changed to PME and the test passes with this change.<br>
<br>
The implication is that reference trajectory computed using cut-off<br>
"matches" with newly calculated trajectory using more accurate PME<br>
method. You can see more details below. **So did the tests really pass?**<br>
<br>
We understand energies, virials and forces are compared for all tests to<br>
report errors/failures.<br>
<br>
<br>
When we searched archives we did not find clear solutions to<br>
test-failure-problems. Wiki site does not give any further guidance.<br>
We have looked at wiki site.<br>
<br>
In the presence of failures it is not clear how to proceed further.<br>
<br>
Kindly guide us in upgrading to gmx 4.04 and "clearing" the tests.<br>
regards,<br>
Sasidhar<br>
<br>
<br>
<br>
<br>
<br>
==========================================================================<br>
This is the output (before making any changes), when i get when i run the<br>
test script gmxtest.pl for 4.0.4 on gromacs-4.0.4.<br>
<br>
$ ./gmxtest.pl all<br>
All 16 simple tests PASSED<br>
FAILED. Check files in field<br>
FAILED. Check files in tip4p<br>
FAILED. Check files in tip4pflex<br>
FAILED. Check files in water<br>
4 out of 14 complex tests FAILED<br>
FAILED. Check files in kernel020<br>
FAILED. Check files in kernel120<br>
FAILED. Check files in kernel121<br>
FAILED. Check files in kernel122<br>
FAILED. Check files in kernel123<br>
FAILED. Check files in kernel124<br>
FAILED. Check files in kernel220<br>
FAILED. Check files in kernel221<br>
FAILED. Check files in kernel222<br>
FAILED. Check files in kernel223<br>
FAILED. Check files in kernel224<br>
FAILED. Check files in kernel320<br>
FAILED. Check files in kernel321<br>
FAILED. Check files in kernel322<br>
FAILED. Check files in kernel323<br>
FAILED. Check files in kernel324<br>
16 out of 63 kernel tests FAILED<br>
N Reference This test<br>
10 -33.9883 -29.4637<br>
11 -33.9883 -29.4637<br>
There were 2 differences in final energy with the reference file<br>
All 45 pdb2gmx tests PASSED<br>
pdb2gmx tests FAILED<br>
<br>
<br>
The tests which failed previously, passed when following changes were made<br>
to the grompp.mdp files of the failed test directories.<br>
<br>
1) field : coulombtype : cut-off to PME<br>
2) tip4p : tempcoupl : berendsen to V-rescale<br>
3) tip4pflex : vdwtype : cut-off to shift<br>
4) water : tempcoupl : yes to V-rescale<br>
<br>
5)kernel020-124 : coulombtype : cut-off to PME & making rlist = rcoulomb<br>
6)kernel220-224 : coulombtype : recation-field-nec to PME & making rlist =<br>
rcoulomb<br>
<br>
7)kernel320-324 : coulombtype : switch to PME & making rlist = rcoulomb.<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Thu, 23 Apr 2009 16:24:39 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] problem in topology file of protein-lipid<br>
bilayer system for grompp<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:49F009A7.9090108@anu.edu.au">49F009A7.9090108@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
nitu sharma wrote:<br>
> Dear Justin<br>
><br>
> I am doing simulation of membrane protein .I<br>
> follow your tutorial for that I think its perfect for that. But I am<br>
> getting problem in doing inflategro step, I alredy discuss this problem<br>
> with you but now I am starting everything fresh I have completed upto<br>
> concatanation of protein with lipid bilayer after that for packing of<br>
> lipid around protein I am using inflategro script from teleman website<br>
> . Problem came in second step of inflategro i.e for energy minimisation<br>
> for this I need topology file of "protein-lipid system".<br>
> I am giving you information in detail i.e -<br>
> for topology file I have made changes in topol.top file which I got from<br>
> pdb2gmx command in first step for protein processing ,the topol .top<br>
> file is like this-<br>
> File 'topol.top' was generated<br>
> ; By user: nitu (504)<br>
> ; On host: localhost.localdomain<br>
> ; At date: Thu Apr 16 23:20:48 2009<br>
> ;<br>
> ; This is your topology file<br>
> ; Grunge ROck MAChoS<br>
> ;<br>
> ; Include forcefield parameters<br>
> #include "ffG53a6.itp"<br>
><br>
> ; Include chain topologies<br>
> #include "topol_A.itp"<br>
> #include "topol_B.itp"<br>
><br>
> ; Include water topology<br>
> #include "spc.itp"<br>
><br>
> #ifdef POSRES_WATER<br>
> ; Position restraint for each water oxygen<br>
> [ position_restraints ]<br>
> ; i funct fcx fcy fcz<br>
> 1 1 1000 1000 1000<br>
> #endif<br>
><br>
> ; Include generic topology for ions<br>
> #include "ions.itp"<br>
><br>
> [ system ]<br>
> ; Name<br>
> Grunge ROck MAChoS<br>
><br>
> [ molecules ]<br>
> ; Compound #mols<br>
> Protein_A 1<br>
> Protein_B 1<br>
> **********<br>
> And the change topology file is like this-<br>
><br>
> ; Include forcefield parameters<br>
> #include "ffG53a6_lipid.itp"<br>
><br>
> ; Include chain topologies<br>
> #include "topol_A.itp"<br>
> #include "topol_B.itp"<br>
><br>
> #ifdef POSRES<br>
> #include "posre_A.itp"<br>
> #include "posre_B.itp"<br>
> #endif<br>
<br>
I think you've been told before that this is garbage.<br>
[position_restraints] directives are components of a [moleculetype], and<br>
so must come before the [moleculetype] of a subsequent molecule. Your<br>
use of the last four #include preprocessing commands violates this. You<br>
should make two #ifdef POSRES sections appropriately.<br>
<br>
> ; Include DMPC chain topology<br>
> #include "dmpc.itp"<br>
><br>
><br>
> [ system ]<br>
> ; Name<br>
> Protein in DMPC bilayer<br>
><br>
> [ molecules ]<br>
> ; Compound #mols<br>
> Protein_A 1<br>
> Protein_B 1<br>
> DMPC 128<br>
><br>
> but when I gave this topology file to grompp it shws error-<br>
> no. of coordinates in coordinate file doesn,t mach the topology file .<br>
<br>
OK, so do the arithmetic and see what the problem is.<br>
<br>
> Can you suggest me something for making topology file for protein-lipid<br>
> bilayer system. Is there any other method for making topology file ,I<br>
> have read in mannual chapter 5 but there is also mentioned same method.<br>
> If possible please help me becoz without solving this problem I can't<br>
> move for furthur processing .<br>
><br>
> * My gro file of protein shows 9902 atoms .<br>
> As you ask in previous mail is .itp file have [ molecules ] section the<br>
> answer is the .itp file haven't molecules section it have [molecule type<br>
> ] section can it also create problem for topology file working.<br>
<br>
So you have 9902 atoms in your coordinate file. How many atoms are in<br>
protein A, protein B and the 128 copies of DMPC *according to their<br>
[moleculetype] definitions*?<br>
<br>
Mark</blockquote><div>Dear Mark<br>Thanks for your reply. as u ask- how many atoms is------Protein A- 5244<br> protein B- 4658<br> And in one dmpc molecule there is 46 atoms so in 128 it is 5888 atoms<br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
can u suggest me how it is helpful in making correct topology file.</blockquote><div>As you wrote in your mail you should make two # ifdef POSRES section does it means separatly before addind .itp file of Protein A and Protein B???????? <br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
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End of gmx-users Digest, Vol 60, Issue 116<br>
******************************************<br>
</blockquote></div><br>