date:20140819

[gmx-users] How do you print positions in double precision

2014-08-19 Thread Jackson Chief Elk

Hi,
I have gone through the procedure of installing version 5.0 in double 
precision with CMAKE, however the positions are still printing in single 
precision mode.  I need the extra precision to calculate dipole correlation 
function for confined water system, anybody run into this precision issue?
Cheers,
Jackson
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Re: [gmx-users] Most appropriate structure to compare to in g_rms

2014-08-19 Thread Natalie Stephenson

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin 
Lemkul [jalem...@vt.edu]
Sent: 18 August 2014 17:47
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Most appropriate structure to compare to in g_rms

On 8/18/14, 9:41 AM, Natalie Stephenson wrote:
 Hi all,

 This probably seems a really obvious question, but I'm struggling to get my
 head around it. I am performing simulations to determine the effect of
 mutations on key regions of the protein. I have a crystal structure which I
 am using as the WT construct, and have performed homology modelling to create
 the point mutations of interest.

 I have used g_rms using the Production MD .tpr as the reference to look at
 the change in movement for key regions of the structure, comparing the degree
 of movement with the WT and mutated construct. Unfortunately, this does not
 necessarily tell me about changes occuring, for example, one key region is
 showing no change in RMSD however is displaced compared to that in the WT.

Can you provide your exact command(s) and the groups chosen for fitting and
output?  The outcome is highly dependent upon proper choices being made.

The commands I have been using are:
1. g_rms -s prodMD.tpr -f prodMD.xtc -n index.ndx -tu ns -o prodMD_RMSD.xvg (to 
compare to equilibrate structure)
2. g_rms -s EM.tpr -f prodMD.xtc -n index.ndx -tu ns -o prodMDtoEM_RMSD.xvg (to 
compare to crystal structure)

In both cases I have been chosing protein for the least square fit and then the 
specific region for the fit, though I'm not sure this is correct. What is the 
best way of knowing which is the proper choice for this? Is there any good 
resources I could access to read up on this? 

 Would it be better to use the WT EM.tpr as the reference structure for
 everything (i.e. compare everything to the WT crystal structure)? Obviously
 these topologies will have slightly different numbers of atoms etc. will this
 be a problem?

This will be a problem.  You can get around it, though, by using tpbconv (gmx
convert-tpr in 5.0) to extract just backbone atoms from both .tpr files and
trajectories.  If you don't, g_rms will complain about mismatching atom numbers
or you will be mapping the wrong atoms in the trajectory since the two proteins
have different numbers of atoms.

Also note that g_rmsf is probably useful here, too, as you can get per-residue
fluctuations and RMSD.

-Justin

This is what I had thought - I'll definitely try using tpbconv to fit the 
backbones and look into changes. Though some of the changes I am interested in 
are the sidechain movements. I'll definitely try the g_rmsf for this.
Thanks so much for all the help!

Natalie

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] g_dielectric error

2014-08-19 Thread Cyrus Djahedi

Hey everyone. Im looking to run g_dielectric on my total dipole moment ACF 
(dipcorr.xvg) by:

g_dielectric -f dipcorr.xvg

I get the following error message. Does anyone know what parameter they are 
referring to?

WARNING: non-polarizable models can never yield an infinite
dielectric constant that is different from 1. This is incorrect
in the reference given above (Spoel98a).

Read data set containing 2 colums and 5001 rows
Assuming (from data) that timestep is 1, nxtail = 500
Creating standard deviation numbers ...
nbegin = 5, x[nbegin] = 5, tbegin = 5
Step   chi^2  Lambda  A1  A2  A3 A4
   0  1.04737e+10  1.0e-02  0.0e+00
   1  1.04737e+10  1.0e-01  0.0e+00
   2  1.04737e+10  1.0e+00  0.0e+00
   3  1.04737e+10  1.0e+01  0.0e+00
   4  1.04737e+10  1.0e+02  0.0e+00
   5  1.04737e+10  1.0e+03  0.0e+00
   6  1.04737e+10  1.0e+04  0.0e+00
   7  1.04737e+10  1.0e+05  0.0e+00
   8  1.04737e+10  1.0e+06  0.0e+00
   9  1.04737e+10  1.0e+07  0.0e+00
  10  1.04737e+10  1.0e+08  0.0e+00
  11  1.04737e+10  1.0e+09  0.0e+00
  12  1.04737e+10  1.0e+10  0.0e+00
  13  1.04737e+10  1.0e+11  0.0e+00
  14  1.04737e+10  1.0e+12  0.0e+00
  15  1.04737e+10  1.0e+13  0.0e+00
  16  1.04737e+10  1.0e+14  0.0e+00
  17  1.04737e+10  1.0e+15  0.0e+00
  18  1.04737e+10  1.0e+16  0.0e+00
  19  1.04737e+10  1.0e+17  0.0e+00
  20  1.04737e+10  1.0e+18  0.0e+00
  21  1.04737e+10  1.0e+19  0.0e+00
  22  1.04737e+10  1.0e+20  0.0e+00
  23  1.04737e+10  1.0e+21  0.0e+00
  24  1.04737e+10  1.0e+22  0.0e+00
  25  1.04737e+10  1.0e+23  0.0e+00
  26  1.04737e+10  1.0e+24  0.0e+00
  27  1.04737e+10  1.0e+25  0.0e+00
  28  1.04737e+10  1.0e+26  0.0e+00
  29  1.04737e+10  1.0e+27  0.0e+00
  30  1.04737e+10  1.0e+28  0.0e+00
  31  1.04737e+10  1.0e+29  0.0e+00
  32  1.04737e+10  1.0e+30  0.0e+00
  33  1.04737e+10  1.0e+31  0.0e+00
  34  1.04737e+10  1.0e+32  0.0e+00
  35  1.04737e+10  1.0e+33  0.0e+00
  36  1.04737e+10  1.0e+34  0.0e+00
  37  1.04737e+10  1.0e+35  0.0e+00
  38  1.04737e+10  1.0e+36  0.0e+00
  39  1.04737e+10  1.0e+37  0.0e+00
  40  1.04737e+10  1.0e+38  0.0e+00
  41  1.04737e+10 inf  0.0e+00
  42  1.04737e+10 inf  0.0e+00
  43  1.04737e+10 inf  0.0e+00
  44  1.04737e+10 inf  0.0e+00
  45  1.04737e+10 inf  0.0e+00
  46  1.04737e+10 inf  0.0e+00
  47  1.04737e+10 inf  0.0e+00
  48  1.04737e+10 inf  0.0e+00
  49  1.04737e+10 inf  0.0e+00


---
Program g_dielectric, VERSION 4.6.1
Source code file: /home/cyrusdja/Downloads/gromacs-4.6.1/src/tools/expfit.c, 
line: 570

Fatal error:
nparm = 0 in file /home/cyrusdja/Downloads/gromacs-4.6.1/src/tools/expfit.c, 
line 571
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

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[gmx-users] g_sas dG

2014-08-19 Thread xy21hb

Dear all,


I just wanna calculate the SAS of a protein (ubiquitin) in a protein-in-water 
binary system,
when I use g_sas, it asks me for a caculation group and output group,
I chose the whole protein as both groups.

However, the solvation free energy (dG) is positive and a bit large, ~ +300 
KJ/mol,
I would imagine solvating a protein, in general, should stabilize the protein.
Is that true and how accurate is the dG compared to that from other methods 
lsuch as thermal integration, ...? 

Thanks,

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Re: [gmx-users] g_sas dG

2014-08-19 Thread David van der Spoel


On 2014-08-19 11:30, xy21hb wrote:

Dear all,


I just wanna calculate the SAS of a protein (ubiquitin) in a protein-in-water 
binary system,
when I use g_sas, it asks me for a caculation group and output group,
I chose the whole protein as both groups.

However, the solvation free energy (dG) is positive and a bit large, ~ +300 
KJ/mol,
I would imagine solvating a protein, in general, should stabilize the protein.
Is that true and how accurate is the dG compared to that from other methods 
lsuch as thermal integration, ...?

Thanks,

Do not trust these results at face value. Besides the model being very 
crude to begin with, the implementation needs checking as well. It might 
just be the sign though, you can compare the values in the data file 
(dgsolv.dat IIRC) to the paper to begin with.


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU?

2014-08-19 Thread Kester Wong

Hi Justin,After some googling, and tweaking with the mdp parameters (step size), I think I have managed to produce the ener.edr and ultimately the ener.xvg files.Anyway, the same problem occured at the same atom each time after an energy minimisation calculation, pointing at the same atom, irregardless of my "emstep".So, I went to my structure(.gro) file and made some changes to the problematic atom (atom 33772) by moving the atomic coordinates of 33772, 33773 and 33774 along the z-direction. I did that because the atom belongs to a water molecule.After that, the "ndx" and "tpr" files were updated.The subsequent energy minimisation based on the amended "gro" file fixed the issue, albeit with further corrections to other atoms/molecules.The confout.gro and ener.edr files were then produced alright.Kester- 원본 메일 -보낸사람 : Kester Wong kester2...@ibs.re.kr받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 8월 19일(화) 11:57:30제목 : Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU?Hi Justin,I think I might have used a pretty small Fmax value for my system of 2000+ water molecules.The md.log file reports:Steepest Descents converged to machine precision in 14 steps,but did not reach the requested Fmax 200.Potential Energy = 7.9771407e+19Maximum force = inf on atom 33772Norm of force = infI guess this issue would be corrected using emtol = 1000?Regards,Kester- 원본 메일 -보낸사람 : Justin Lemkul jalem...@vt.edu받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 8월 19일(화) 01:44:08제목 : Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU?On 8/18/14, 8:15 AM, Kester Wong wrote:
Hi Justin,

THanks for the quick reply. I am concerned that it might be the ener.edr file
that is fragmented, as the md.log report seem fine.

Also, the same problem persisted even when the input files were migrated to a
new folder for an energy minimisation calculation.

For the second energy minimisation calculation, I even re-generated the
system.ndx and topol.tpr files.

Are sensible energies reported in the corresponding .log file? A run may
"finish" but yield infinite energies if something failed. That can also lead to
an incorrect interpretation of .edr contents. Again, running gmxcheck on all
output files can be useful here.

-Justin

Regards,

Kester

- 원본 메일 -

*보낸사람* : Justin Lemkul
*받는사람* :
*받은날짜* : 2014년 8월 18일(월) 20:56:56
*제목* : Re: [gmx-users] Energy file ener.edr not recognized, maybe
different CPU?

On 8/18/14, 7:43 AM, Kester Wong wrote:
Dear all,

After the energy minimisation calculation, I plotted the (energy vs time)
profile for some structures with the ener.xvg file.

However, of all the energy minimised structures I have, one did not work.

I have been trying to convert the energy minimised file "ener.edr" to "ener.xvg"
using the command: g_energy_mpi -f ener.edr -o ener.xvg

As the same procedure worked for all my other structures, this fatal error read:

Program g_energy_mpi, VERSION 5.0

Source code file: /home/choimin/Gromacs/gromacs-5.0/src/gromacs/fileio/enxio.c,
line: 822

Fatal error:

Energy file ener.edr not recognized, maybe different CPU?

The xvg file was successfully produced for other structures, why did it fail on
this particular system?

Investigate the .log file and run gmxcheck on all of the output files of the
problematic run. Likely it failed and produced fragmented output.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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