Re: [gmx-users] double precision

[Justin A. Lemkul]

abhijit kayal wrote:

Hi,
I am going to do the normal mode analysis of 1OMB.pdb.For this purpose I 
have to run the GROMACS in double precision .For this i went through the 
manual and made necessart changes in .mdp file.But when I gave grompp_d 
it showed like this
[abhi...@scfbioserver 1omb]$ grompp_d -v -f em.mdp -c b4em.gro -o em.tpr 
-p 1OMB.top

-bash: grompp_d: command not found.
 I am using GROMACS 4.0.4 version .So my question is why 
it showed like this.
  


Did you specify --program-suffix=_d when doing the double-precision 
installation?

-Justin



Thank you
  
Abhijit Kayal
  
IIT Delhi





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Justin A. Lemkul
Ph.D. Candidate
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


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Re: [gmx-users] RE: Re: g_energy and g_analyze give different averages

[Justin A. Lemkul]

Ragnarok sdf wrote:



I am terribly sorry. I have not expressed myself well. I meant the 
standard error of the mean energy given by g_energy. So I believe I 
would like to know the standard error estimate.


Based on the output RMSD (standard deviation), it seems rather straightforward 
to calculate SE:


http://en.wikipedia.org/wiki/Standard_error_(statistics)#Standard_error_of_the_mean

-Justin




I don't understand what you want exactly.
Your g_energy command does exponential averaging, that happens
on the printed data points. So there g_analyze or any program will
do fine.
For the original data g_energy gives the exact standard deviation
over all MD steps, called RMSD.

But do you really want the standard deviation, or do you want
a standard error estimate?

Berk

Date: Fri, 28 Aug 2009 09:30:37 -0300
From: fabrac...@gmail.com 
To: gmx-users@gromacs.org 
Subject: [gmx-users] Re: g_energy and g_analyze give different averages


Is there a correct way to obtain the standard deviation for these
data sets?




 >

 > Ragnarok sdf wrote:

 > > When analysing FEP simulations. After running g_energy -f
fep000.edr -f2

 > > fep_000-005.edr for obtaining the dF = -kT ln <
exp(-(EB-EA)/kT) >A I

 > tried

 > > to obtain the standard deviation for this ensemble average using

 > g_analyze

 > > -f runavg.xvg, but I've noticed that the average values are quite

 > different

 > >

 > >

 > g_energy takes all values during your simulation into account,
g_analyze

 > only the printed datapoints.

 >

 >






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Justin A. Lemkul
Ph.D. Candidate
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


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[gmx-users] RE: Re: g_energy and g_analyze give different averages

[Ragnarok sdf]

I am terribly sorry. I have not expressed myself well. I meant the standard
error of the mean energy given by g_energy. So I believe I would like to
know the standard error estimate.

>
> I don't understand what you want exactly.
> Your g_energy command does exponential averaging, that happens
> on the printed data points. So there g_analyze or any program will do fine.
> For the original data g_energy gives the exact standard deviation
> over all MD steps, called RMSD.
>
> But do you really want the standard deviation, or do you want
> a standard error estimate?
>
> Berk
>
> Date: Fri, 28 Aug 2009 09:30:37 -0300
> From: fabrac...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: g_energy and g_analyze give different averages
>
>
> Is there a correct way to obtain the standard deviation for these data
> sets?
>
>
>
>
> >
>
> > Ragnarok sdf wrote:
>
> > > When analysing FEP simulations. After running g_energy -f fep000.edr
> -f2
>
> > > fep_000-005.edr for obtaining the dF = -kT ln < exp(-(EB-EA)/kT) >A I
>
> > tried
>
> > > to obtain the standard deviation for this ensemble average using
>
> > g_analyze
>
> > > -f runavg.xvg, but I've noticed that the average values are quite
>
> > different
>
> > >
>
> > >
>
> > g_energy takes all values during your simulation into account, g_analyze
>
> > only the printed datapoints.
>
> >
>
> >
>
>
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Re: [gmx-users] gmxtest failures OK?

[Warren Gallin]

I could only find the 4.0.4 tests, which are what I ran.

Where would I find the latest tests?

Warren Gallin

On 28-Aug-09, at 3:42 PM, Justin A. Lemkul wrote:



Which test set are you using?  These failures are to be expected for  
earlier versions in the 4.0.x series, but were fixed in a 4.0.5- 
compatible version.  I don't believe these failures ever indicated  
anything truly wrong, but the newest version has different (clearer  
and more detailed) output and all the tests should pass.


-Justin

Warren Gallin wrote:

Hi,
   I just installed v. 4.0.5
   Wen I ran the gmxtests I got the following output:
All 16 simple tests PASSED
All 14 complex tests PASSED
FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
All 45 pdb2gmx tests PASSED
Am I correct in thinking that these kernel failures are expected,  
and therefore that the installation worked?

Thanks,
Warren Gallin
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--


Justin A. Lemkul
Ph.D. Candidate
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


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Re: [gmx-users] gmxtest failures OK?

[Justin A. Lemkul]

Warren Gallin wrote:

I could only find the 4.0.4 tests, which are what I ran.

Where would I find the latest tests?



It used to be linked from the wiki, but the site is still down and I can't find 
it on the main page.  I imagine you could pull down the latest development 
version (which should have all the 4.0.5-relevant changes implemented) from the 
git repository.  Instructions are here:


http://www.gromacs.org/Developers/Git/Basic_Git_Usage

-Justin


Warren Gallin

On 28-Aug-09, at 3:42 PM, Justin A. Lemkul wrote:



Which test set are you using?  These failures are to be expected for 
earlier versions in the 4.0.x series, but were fixed in a 
4.0.5-compatible version.  I don't believe these failures ever 
indicated anything truly wrong, but the newest version has different 
(clearer and more detailed) output and all the tests should pass.


-Justin

Warren Gallin wrote:

Hi,
   I just installed v. 4.0.5
   Wen I ran the gmxtests I got the following output:
All 16 simple tests PASSED
All 14 complex tests PASSED
FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
All 45 pdb2gmx tests PASSED
Am I correct in thinking that these kernel failures are expected, and 
therefore that the installation worked?

Thanks,
Warren Gallin
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--


Justin A. Lemkul
Ph.D. Candidate
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


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--


Justin A. Lemkul
Ph.D. Candidate
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


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Re: [gmx-users] Re: SIMULATION OF GOLD NANOPARTICLE

[George Tsigaridas]

Thank you Justin. A very interesting paper. Next time, if I want to search 
for something I 'll call you ... :)


Thanks again

George


- Original Message - 
From: "Justin A. Lemkul" 

To: "Discussion list for GROMACS users" 
Sent: Saturday, August 29, 2009 1:30 AM
Subject: Re: [gmx-users] Re: SIMULATION OF GOLD NANOPARTICLE





George Tsigaridas wrote:

Hi Vitaly

I 've searched in the Web of Science for gold nanoparticles and Gromacs
but I didn't get any results. Could you give me some more details on
these publications?


If you don't find what you want, keep searching.  For example, a search in 
WoS

for "gold nanoparticles" AND "molecular dynamics" yields over 80 results.


Are they performed with GROMACS? Which forcefield has been used?



An example of one possibility:

http://dx.doi.org/10.1002/jcc.21165

-Justin


Thank you in advance

George


- Original Message - From: "Vitaly V. Chaban" 


To: 
Sent: Friday, August 28, 2009 10:06 PM
Subject: [gmx-users] Re: SIMULATION OF GOLD NANOPARTICLE



Hi George,

I know some attempts of gold nanosize particles simulation published
during the last years. Did you explore the literature?

~ Vitaly



Hi GROMACS users

Does anyone have any information on the simulation of gold
nanoparticles with GROMACS?

Thank you in advance

George

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Internal Virus Database is out of date.
Checked by AVG - www.avg.com
Version: 8.5.392 / Virus Database: 270.13.58/2304 - Release Date:
08/15/09 06:10:00

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--


Justin A. Lemkul
Ph.D. Candidate
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


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06:10:00


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Re: [gmx-users] Re: SIMULATION OF GOLD NANOPARTICLE

[Justin A. Lemkul]

George Tsigaridas wrote:

Hi Vitaly

I 've searched in the Web of Science for gold nanoparticles and Gromacs 
but I didn't get any results. Could you give me some more details on 
these publications?


If you don't find what you want, keep searching.  For example, a search in WoS 
for "gold nanoparticles" AND "molecular dynamics" yields over 80 results.



Are they performed with GROMACS? Which forcefield has been used?



An example of one possibility:

http://dx.doi.org/10.1002/jcc.21165

-Justin


Thank you in advance

George


- Original Message - From: "Vitaly V. Chaban" 
To: 
Sent: Friday, August 28, 2009 10:06 PM
Subject: [gmx-users] Re: SIMULATION OF GOLD NANOPARTICLE



Hi George,

I know some attempts of gold nanosize particles simulation published
during the last years. Did you explore the literature?

~ Vitaly



Hi GROMACS users

Does anyone have any information on the simulation of gold 
nanoparticles with GROMACS?


Thank you in advance

George

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Internal Virus Database is out of date.
Checked by AVG - www.avg.com
Version: 8.5.392 / Virus Database: 270.13.58/2304 - Release Date: 
08/15/09 06:10:00


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--


Justin A. Lemkul
Ph.D. Candidate
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


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Re: [gmx-users] Re: SIMULATION OF GOLD NANOPARTICLE

[George Tsigaridas]

Hi Vitaly

I 've searched in the Web of Science for gold nanoparticles and Gromacs but 
I didn't get any results. Could you give me some more details on these 
publications?

Are they performed with GROMACS? Which forcefield has been used?

Thank you in advance

George


- Original Message - 
From: "Vitaly V. Chaban" 

To: 
Sent: Friday, August 28, 2009 10:06 PM
Subject: [gmx-users] Re: SIMULATION OF GOLD NANOPARTICLE



Hi George,

I know some attempts of gold nanosize particles simulation published
during the last years. Did you explore the literature?

~ Vitaly



Hi GROMACS users

Does anyone have any information on the simulation of gold nanoparticles 
with GROMACS?


Thank you in advance

George

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Checked by AVG - www.avg.com
Version: 8.5.392 / Virus Database: 270.13.58/2304 - Release Date: 08/15/09 
06:10:00


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Re: [gmx-users] gmxtest failures OK?

[Justin A. Lemkul]

Which test set are you using?  These failures are to be expected for earlier 
versions in the 4.0.x series, but were fixed in a 4.0.5-compatible version.  I 
don't believe these failures ever indicated anything truly wrong, but the newest 
version has different (clearer and more detailed) output and all the tests 
should pass.


-Justin

Warren Gallin wrote:

Hi,

I just installed v. 4.0.5

Wen I ran the gmxtests I got the following output:


All 16 simple tests PASSED
All 14 complex tests PASSED
FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
All 45 pdb2gmx tests PASSED


Am I correct in thinking that these kernel failures are expected, and 
therefore that the installation worked?


Thanks,

Warren Gallin

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--


Justin A. Lemkul
Ph.D. Candidate
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


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Re: [gmx-users] mdrun segmentation fault

[Justin A. Lemkul]

sunny mishra wrote:

Dear all,

At the final step of my mdrun I get LINCS warning. I don't know whats 
the issue. Please help me out.





If I had a nickel for every time I saw a LINCS warning on this list... :)

The answer is always the same.  There is something physically unrealistic about 
your simulation such that it is "blowing up."  See here:


http://www.gromacs.org/WIKI-import/Blowing_Up

And the relevant entry here:

http://www.gromacs.org/WIKI-import/Main_Page/Errors

-Justin


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 51.050964, max 314.598846 (between atoms 3 and 4)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 51 52   90.00.2700  16.3676  0.2700  
 51 53   90.00.2700  17.4243  0.2700  
 52 53   90.20.2700   2.1691  0.2700  
 57 58   90.00.2700  19.9248  0.2700  
 57 59   90.00.2700  27.7437  0.2700  
 58 59   89.90.2700   9.5994  0.2700  
 67 68   89.10.2700  11.0711  0.2700  
 67 69   89.50.2700  17.3915  0.2700  
 68 69   89.10.2700   8.9722  0.2700  
 68 70   88.70.2700   7.4897  0.2700  
 69 70   89.10.2700  10.5427  0.2700  
 74 75   90.00.2700  15.9658  0.2700  
 74 76   90.00.2700  14.3261  0.2700  
 75 76   90.00.2700  15.3014  0.2700  
 78 79   53.00.2700   0.3682  0.2700  
 78 80   36.00.2700   0.2621  0.2700  
 79 80   78.80.2700   0.3108  0.2700  
 79 81   74.60.2700   0.2500  0.2700  
 96 97   90.00.2700   5.6881  0.2700  
 96 98   90.00.2700  12.4635  0.2700  
 97 98   90.00.2700  12.2473  0.2700  
105106   92.00.2700   5.3689  0.2700  
105107   90.90.2700   4.9643  0.2700  
106107   89.50.2700   5.2502  0.2700  
106108   90.20.2700  12.9074  0.2700  
107108   89.80.2700  13.3348  0.2700  
123124   90.00.2700   0.3295  0.2700  
123125   90.00.2700   0.4033  0.2700  
124125   90.00.2700   0.4582  0.2700  
134135   89.80.2700   7.5418  0.2700  
134136   89.80.2700   7.6180  0.2700  
135136   89.80.2700   7.5943  0.2700  
177178   90.00.2700  21.0157  0.2700  
177179   90.00.2700  21.3382  0.2700  
178179   90.00.2700   5.0506  0.2700  
206207   90.10.2700   3.7166  0.2700  
206208   90.00.2700  17.1633  0.2700  
207208   90.00.2700  14.3937  0.2700  
210211   90.00.2700   1.4919  0.2700  
210212   90.00.2700   1.4477  0.2700  
229230   89.90.2700  46.6891  0.2700  
229231   89.80.2700  12.4685  0.2700  
230231   89.90.2700  34.3535  0.2700  
233234   90.00.2700  17.0640  0.2700  
233235   90.00.2700  12.0837  0.2700  
234235   90.00.2700  21.1578  0.2700  
240241   90.10.2700  14.3404  0.2700  
240242   89.90.2700   5.5938  0.2700  
241242   89.50.2700  10.7072  0.2700  
241243   90.10.2700  11.1853  0.2700  
242243   89.90.2700  14.6316  0.2700  
278279   90.40.2700   0.4126  0.2700  
278280   90.30.2700   0.6367  0.2700  
279280   90.30.2700   0.6632  0.2700  
321322   90.10.2700  13.7866  0.2700  
321323   90.10.2700   8.6467  0.2700  
322323   90.10.2700   6.2637  0.2700  
325327   89.90.2700   5.2665  0.2700  
326327   89.90.2700   5.3472  0.2700  
343344   90.20.2700   5.8168  0.2700  
343345   90.50.2700   5.0440  0.2700  
344345   90.20.2700   5.9636  0.2700  
344346   89.70.2700   6.8436  0.2700  
345346   89.50.2700   2.4697  0.2700  
364365   89.90.2700   1.8601  0.2700  
364366   90.00.2700   2.8203  0.2700  
365366   89.90.2700   1.4138  0.2700  
389390   90.00.2700   0.4660  0.2700  
389391   90.00.2700   0.4625  0.2700  
390391   90.00.2700   0.4644  0.2700  
417418   89.90.2700   3.9010  0.2700  
417419   89.90.2700   3.8294  0.2700  
418  

[gmx-users] gmxtest failures OK?

[Warren Gallin]

Hi,

I just installed v. 4.0.5

Wen I ran the gmxtests I got the following output:


All 16 simple tests PASSED
All 14 complex tests PASSED
FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
All 45 pdb2gmx tests PASSED


Am I correct in thinking that these kernel failures are expected, and  
therefore that the installation worked?


Thanks,

Warren Gallin

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[gmx-users] mdrun segmentation fault

[sunny mishra]

Dear all,

At the final step of my mdrun I get LINCS warning. I don't know whats the
issue. Please help me out.


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 51.050964, max 314.598846 (between atoms 3 and 4)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 51 52   90.00.2700  16.3676  0.2700
 51 53   90.00.2700  17.4243  0.2700
 52 53   90.20.2700   2.1691  0.2700
 57 58   90.00.2700  19.9248  0.2700
 57 59   90.00.2700  27.7437  0.2700
 58 59   89.90.2700   9.5994  0.2700
 67 68   89.10.2700  11.0711  0.2700
 67 69   89.50.2700  17.3915  0.2700
 68 69   89.10.2700   8.9722  0.2700
 68 70   88.70.2700   7.4897  0.2700
 69 70   89.10.2700  10.5427  0.2700
 74 75   90.00.2700  15.9658  0.2700
 74 76   90.00.2700  14.3261  0.2700
 75 76   90.00.2700  15.3014  0.2700
 78 79   53.00.2700   0.3682  0.2700
 78 80   36.00.2700   0.2621  0.2700
 79 80   78.80.2700   0.3108  0.2700
 79 81   74.60.2700   0.2500  0.2700
 96 97   90.00.2700   5.6881  0.2700
 96 98   90.00.2700  12.4635  0.2700
 97 98   90.00.2700  12.2473  0.2700
105106   92.00.2700   5.3689  0.2700
105107   90.90.2700   4.9643  0.2700
106107   89.50.2700   5.2502  0.2700
106108   90.20.2700  12.9074  0.2700
107108   89.80.2700  13.3348  0.2700
123124   90.00.2700   0.3295  0.2700
123125   90.00.2700   0.4033  0.2700
124125   90.00.2700   0.4582  0.2700
134135   89.80.2700   7.5418  0.2700
134136   89.80.2700   7.6180  0.2700
135136   89.80.2700   7.5943  0.2700
177178   90.00.2700  21.0157  0.2700
177179   90.00.2700  21.3382  0.2700
178179   90.00.2700   5.0506  0.2700
206207   90.10.2700   3.7166  0.2700
206208   90.00.2700  17.1633  0.2700
207208   90.00.2700  14.3937  0.2700
210211   90.00.2700   1.4919  0.2700
210212   90.00.2700   1.4477  0.2700
229230   89.90.2700  46.6891  0.2700
229231   89.80.2700  12.4685  0.2700
230231   89.90.2700  34.3535  0.2700
233234   90.00.2700  17.0640  0.2700
233235   90.00.2700  12.0837  0.2700
234235   90.00.2700  21.1578  0.2700
240241   90.10.2700  14.3404  0.2700
240242   89.90.2700   5.5938  0.2700
241242   89.50.2700  10.7072  0.2700
241243   90.10.2700  11.1853  0.2700
242243   89.90.2700  14.6316  0.2700
278279   90.40.2700   0.4126  0.2700
278280   90.30.2700   0.6367  0.2700
279280   90.30.2700   0.6632  0.2700
321322   90.10.2700  13.7866  0.2700
321323   90.10.2700   8.6467  0.2700
322323   90.10.2700   6.2637  0.2700
325327   89.90.2700   5.2665  0.2700
326327   89.90.2700   5.3472  0.2700
343344   90.20.2700   5.8168  0.2700
343345   90.50.2700   5.0440  0.2700
344345   90.20.2700   5.9636  0.2700
344346   89.70.2700   6.8436  0.2700
345346   89.50.2700   2.4697  0.2700
364365   89.90.2700   1.8601  0.2700
364366   90.00.2700   2.8203  0.2700
365366   89.90.2700   1.4138  0.2700
389390   90.00.2700   0.4660  0.2700
389391   90.00.2700   0.4625  0.2700
390391   90.00.2700   0.4644  0.2700
417418   89.90.2700   3.9010  0.2700
417419   89.90.2700   3.8294  0.2700
418419   51.60.2700   0.2606  0.2700
418420   89.60.2700   0.5341  0.2700
419420   89.70.2700   0.7429  0.2700
441442   89.90.2700  13.9652  0.2700
441443   89.90.2700  10.3452  0.2700
442443   89.80.2700   4.5213  0.2700
544545   90.10.2700  15.9781  0.2700
544546   90.10.2700  30.0933  0.2700
545546   90.10.2700  22.2106  0.2700
548549   90.20.2700  25.9365  0.2700
548550   90.70.2700  26.2207  0.2700
549550   90.30.2700  14.0951  0.2700
549551   91.60.2700  11.6914  0.2700
550551   90.30.2700  21.9519  0.2700
553554   90.70.2700   3.3299  0.2700
553555   90.60.2700   3.9172 

Re: [gmx-users] Re: wierd behavior of mdrun

[Justin A. Lemkul]

Payman Pirzadeh wrote:

There is sth strange about this problem which I suspect it might be due to
the mdp file and input. I can run the energy minimization without any
problems (I submit the job and it apparently works using the same submission
script)! But as soon as I prepare the tpr file for MD run, then I run into
this run-without-output trouble.
Again I paste my mdp file below (I want to run an NVT run):



There isn't anything in the .mdp file that suggests you wouldn't get any output. 
 The output of mdrun is buffered, so depending on your settings, you may have 
more frequent output during energy minimization.  There may be some problem with 
the MPI implementation in buffering and communicating data properly.  That's a 
bit of a guess, but it could be happening.


Definitely check with the cluster admin to see if there are any error messages 
reported for the jobs you submitted.


Another test you could do to force a huge amount of data would be to set all of 
your outputs (nstxout, nstxtcout, etc) = 1 and run a much shorter simulation (to 
prevent massive data output!); this would force more continuous data through the 
buffer.


-Justin


cpp  = cpp
include  = -I../top
define   = -DPOSRES

; Run control

integrator   = md
dt   = 0.001   ;1 fs
nsteps   = 300 ;3 ns
comm_mode= linear
nstcomm  = 1

;Output control

nstxout  = 5000
nstlog   = 5000
nstenergy= 5000
nstxtcout= 1500
nstvout  = 5000
nstfout  = 5000
xtc_grps =
energygrps   =

; Neighbour Searching

nstlist  = 10
ns_type  = grid
rlist= 0.9
pbc  = xyz

; Electrostatistics

coulombtype  = PME
rcoulomb = 0.9
;epsilon_r= 1

; Vdw

vdwtype  = cut-off
rvdw = 1.2
DispCorr = EnerPres

;Ewald

fourierspacing  = 0.12
pme_order   = 4
ewald_rtol  = 1e-6
optimize_fft= yes

; Temperature coupling

tcoupl   = v-rescale
ld_seed  = -1
tc-grps  = System
tau_t= 0.1
ref_t= 275

; Pressure Coupling

Pcoupl   = no
;Pcoupltype   = isotropic
;tau_p= 1.0
;compressibility  = 5.5e-5
;ref_p= 1.0
gen_vel  = yes
gen_temp = 275
gen_seed = 173529
constraint-algorithm = Lincs
constraints  = all-bonds
lincs-order  = 4

Regards,

Payman
 


-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Mark Abraham
Sent: August 27, 2009 3:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Re: wierd behavior of mdrun

Vitaly V. Chaban wrote:

Then I believe you have problems with MPI.

Before I experienced something alike on our old system - serial
version worked OK but parallel one failed. The same issue was with
CPMD by the way. Another programs worked fine. I didn't correct that
problem...

On Thu, Aug 27, 2009 at 7:14 PM, Paymon Pirzadeh

wrote:

Yes,
it works when it is run on one processor interactively!


That's fine, but it doesn't mean the problem is with the parallelism, as 
Vitaly suggests. If your cluster filesystem isn't configured properly, 
you will observe these symptoms. Since the submission script was the 
same, MPI worked previously, so isn't likely to be the problem...


Mark


On Thu, 2009-08-27 at 09:23 +0300, Vitaly V. Chaban wrote:

I made a .tpr file for my md run without any problems (using the bottom
mdp file). My job submission script is also the same thing I used for
other jobs which had no problems. But now when I submit this .tpr file,
only an empty log file is generated! The qstat of the cluster shows

that

the job is running, also the processors are 100% engaged while I have

no

outputs!

A standard guess: what about trying to run the single-processor job on
the same cluster? Does it run OK?



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RE: [gmx-users] Re: wierd behavior of mdrun

[Payman Pirzadeh]

There is sth strange about this problem which I suspect it might be due to
the mdp file and input. I can run the energy minimization without any
problems (I submit the job and it apparently works using the same submission
script)! But as soon as I prepare the tpr file for MD run, then I run into
this run-without-output trouble.
Again I paste my mdp file below (I want to run an NVT run):

cpp  = cpp
include  = -I../top
define   = -DPOSRES

; Run control

integrator   = md
dt   = 0.001   ;1 fs
nsteps   = 300 ;3 ns
comm_mode= linear
nstcomm  = 1

;Output control

nstxout  = 5000
nstlog   = 5000
nstenergy= 5000
nstxtcout= 1500
nstvout  = 5000
nstfout  = 5000
xtc_grps =
energygrps   =

; Neighbour Searching

nstlist  = 10
ns_type  = grid
rlist= 0.9
pbc  = xyz

; Electrostatistics

coulombtype  = PME
rcoulomb = 0.9
;epsilon_r= 1

; Vdw

vdwtype  = cut-off
rvdw = 1.2
DispCorr = EnerPres

;Ewald

fourierspacing  = 0.12
pme_order   = 4
ewald_rtol  = 1e-6
optimize_fft= yes

; Temperature coupling

tcoupl   = v-rescale
ld_seed  = -1
tc-grps  = System
tau_t= 0.1
ref_t= 275

; Pressure Coupling

Pcoupl   = no
;Pcoupltype   = isotropic
;tau_p= 1.0
;compressibility  = 5.5e-5
;ref_p= 1.0
gen_vel  = yes
gen_temp = 275
gen_seed = 173529
constraint-algorithm = Lincs
constraints  = all-bonds
lincs-order  = 4

Regards,

Payman
 

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Mark Abraham
Sent: August 27, 2009 3:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Re: wierd behavior of mdrun

Vitaly V. Chaban wrote:
> Then I believe you have problems with MPI.
> 
> Before I experienced something alike on our old system - serial
> version worked OK but parallel one failed. The same issue was with
> CPMD by the way. Another programs worked fine. I didn't correct that
> problem...
> 
> On Thu, Aug 27, 2009 at 7:14 PM, Paymon Pirzadeh
wrote:
>> Yes,
>> it works when it is run on one processor interactively!

That's fine, but it doesn't mean the problem is with the parallelism, as 
Vitaly suggests. If your cluster filesystem isn't configured properly, 
you will observe these symptoms. Since the submission script was the 
same, MPI worked previously, so isn't likely to be the problem...

Mark

>> On Thu, 2009-08-27 at 09:23 +0300, Vitaly V. Chaban wrote:
 I made a .tpr file for my md run without any problems (using the bottom
 mdp file). My job submission script is also the same thing I used for
 other jobs which had no problems. But now when I submit this .tpr file,
 only an empty log file is generated! The qstat of the cluster shows
that
 the job is running, also the processors are 100% engaged while I have
no
 outputs!
>>> A standard guess: what about trying to run the single-processor job on
>>> the same cluster? Does it run OK?
>>>
>>>
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[gmx-users] Re: SIMULATION OF GOLD NANOPARTICLE

[Vitaly V. Chaban]

Hi George,

I know some attempts of gold nanosize particles simulation published
during the last years. Did you explore the literature?

~ Vitaly

>
> Hi GROMACS users
>
> Does anyone have any information on the simulation of gold nanoparticles with 
> GROMACS?
>
> Thank you in advance
>
> George
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Re: [gmx-users] Wiki site

[David van der Spoel]

Justin A. Lemkul wrote:


Hi,

It looks like the wiki site (oldwiki) is not working, and perhaps has 
been that way for several days, when I last tried to access it.


I was able to look up some stuff on the WIKI-Import feature of the new 
site, but all the links within the articles point to wiki.gromacs.org, 
which has not functioned since the new website migration.


Is there any way to access a fully-functioning wiki site?

-Justin

Sorry to say we had four powerdowns this summer... Apparently we forgot 
to restart this box after the last one...


--
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
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[gmx-users] Wiki site

[Justin A. Lemkul]

Hi,

It looks like the wiki site (oldwiki) is not working, and perhaps has been that 
way for several days, when I last tried to access it.


I was able to look up some stuff on the WIKI-Import feature of the new site, but 
all the links within the articles point to wiki.gromacs.org, which has not 
functioned since the new website migration.


Is there any way to access a fully-functioning wiki site?

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
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


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Re: [gmx-users] pdb2gmx problem

[Justin A. Lemkul]

Warren Gallin wrote:

Hi,

I am trying to set up a simulations of short peptides in water, and 
I want to eliminate the electrostatic interactions of the N-terminal 
amino group and the C-terminal carboxyl group by capping them, with 
acetate for the N-terminus and a C-terminal amide.


I built the PDB file using TINKER (see attached file) but when I run:

pdb2gmx -f Gly10_Capped.pdb -water tip3p -ignh



You need to specify -ter and choose "None" to add a capping group.


N-terminus: NH3+
C-terminus: COO-


Here's your hint: pdb2gmx is assigning default (charged) termini, which is not 
what you want.



Now there are 12 residues with 79 atoms

---
Program pdb2gmx, VERSION 4.0


I would recommend upgrading to the latest version (4.0.5) to take advantage of 
bug fixes, especially those pertinent to DD stability.


-Justin


Source code file: pdb2top.c, line: 574

Fatal error:
atom N not found in residue 1ACE while combining tdb and rtp
---

The ACE residue does not have a N atom, either in the pdb file or in 
ffoplsaa.hdb or in ffoplsaa.rtp, so I don't understand what the problem is.


Can someone shed some light on this?


Warren Gallin









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--


Justin A. Lemkul
Ph.D. Candidate
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


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[gmx-users] pdb2gmx problem

[Warren Gallin]

Hi,

	I am trying to set up a simulations of short peptides in water, and I  
want to eliminate the electrostatic interactions of the N-terminal  
amino group and the C-terminal carboxyl group by capping them, with  
acetate for the N-terminus and a C-terminal amide.


I built the PDB file using TINKER (see attached file) but when I run:

pdb2gmx -f Gly10_Capped.pdb -water tip3p -ignh

	and I selected the OPLSAA/L force field (option 5) when prompted, and  
process continues, terminating in a fatal error:


Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/ffoplsaa.rtp
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/aminoacids.dat
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/aminoacids.dat

WARNING: masses will be determined based on residue and atom names,
 this can deviate from the real mass of the atom type
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/atommass.dat

Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
 this can deviate from the real mass of the atom type
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/vdwradii.dat

Entries in vdwradii.dat: 28
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/dgsolv.dat

Entries in dgsolv.dat: 7
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/electroneg.dat

Entries in electroneg.dat: 71
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/elements.dat

Entries in elements.dat: 218
Reading Gly10_Capped.pdb...
Read 'Protein Gly10_Capped built with TINKER/Force Field Explorer', 44  
atoms
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/xlateat.dat

26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 12 residues with 44 atoms

  chain  #res #atoms
  1 ' '12 44

All occupancy fields zero. This is probably not an X-Ray structure
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/ffoplsaa.atp

Atomtype 1
Reading residue database... (ffoplsaa)
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/ffoplsaa.rtp

Residue 56
Sorting it all out...
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/ffoplsaa.hdb
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/ffoplsaa-n.tdb
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/ffoplsaa-c.tdb

Processing chain 1 (44 atoms, 12 residues)
There are 11 donors and 11 acceptors
There are 21 hydrogen bonds
Checking for duplicate atoms
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/specbond.dat

7 out of 7 lines of specbond.dat converted succesfully
N-terminus: NH3+
C-terminus: COO-
Now there are 12 residues with 79 atoms

---
Program pdb2gmx, VERSION 4.0
Source code file: pdb2top.c, line: 574

Fatal error:
atom N not found in residue 1ACE while combining tdb and rtp
---

	The ACE residue does not have a N atom, either in the pdb file or in  
ffoplsaa.hdb or in ffoplsaa.rtp, so I don't understand what the  
problem is.


Can someone shed some light on this?


Warren Gallin



Gly10_Capped.pdb
Description: Binary data



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RE: [gmx-users] continuation

[Berk Hess]

Hi,

-append yes is incorrect, it should be -append without the yes.
In this case this error has no effect though.

Is your trr file larger than 2 GB?
We have fixed a bug with this in the upcoming 4.0.6 release.

Berk

> Date: Fri, 28 Aug 2009 16:48:07 +0200
> From: alexander.h...@mytum.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] continuation
> 
> Hi,
> 
> I'm trying to continue a sim using:
> 
> old cmd line + -cpi state.cpt -append yes
> 
> where old cmd line =
> mpirun -np 1 $GROMACS_T37/mdrun -s shear -c shear_final -g shear_final
> -o shear
> 
> All files exist.
> 
> and I get:
> 
> ---
> Program mdrun, VERSION 4.0.5
> Source code file: checkpoint.c, line: 1248
> 
> Fatal error:
> Truncation of file shear.trr failed.
> ---
> 
> What's the problem??
> 
> Thx,
> Alex
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Re: [gmx-users] question

[Justin A. Lemkul]

delara aghaie wrote:



--- On *Fri, 8/28/09, delara aghaie //* wrote:


From: delara aghaie 
Subject: [gmx-users] question
To: gmx-users@gromacs.org
Date: Friday, August 28, 2009, 2:17 AM

Dear Gromaxs users
I want to plot a graph from a remote computer. My operating system
is windows Vista. I connect to Imperial college in London via VPN
connection. There I do the simulations using gromacs. Now I want to
plot for example the *density.xvg* using gnuplot, but I get this
error:*X connection to localhost:18.0 broken (explicit kill or
server shutdown).*
** 
I should mention that I was able to plot my graphs last week. Now

nothing has changed but I get this error.
I have putty, and Xming installed on my windows.
Thanks for your guiedence
*Delara*
 



There is something broken with the X window configuration.  Contact a system 
admin.  This is not a Gromacs problem.


-Justin




-Inline Attachment Follows-

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--


Justin A. Lemkul
Ph.D. Candidate
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


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Re: [gmx-users] multiple T-Coupling groups

[Justin A. Lemkul]

simon sangma wrote:


---
Program grompp, VERSION 4.0.4
Source code file: readir.c, line: 1058

Fatal error:
Atom 1 in multiple T-Coupling groups (1 and 2)
---


The error message is quite clear; it even tells you which atom is problematic. 
Without seeing the .mdp and .ndx files, there's not much more anyone can do to help.


-Justin



"Wild Pointers Couldn't Drag Me Away" (K.A. Feenstra)




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--


Justin A. Lemkul
Ph.D. Candidate
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


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[gmx-users] continuation

[aherz]

Hi,

I'm trying to continue a sim using:

old cmd line + -cpi state.cpt -append yes

where old cmd line =
mpirun -np 1 $GROMACS_T37/mdrun -s shear -c shear_final -g shear_final
-o shear

All files exist.

and I get:

---
Program mdrun, VERSION 4.0.5
Source code file: checkpoint.c, line: 1248

Fatal error:
Truncation of file shear.trr failed.
---

What's the problem??

Thx,
Alex
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[gmx-users] RE: Re: g_energy and g_analyze give different averages

[Ragnarok sdf]

I am terribly sorry. I have not expressed myself well. I meant the standard
error of the mean energy given by g_energy. So I believe I would like to
know the standard error estimate.

>
> I don't understand what you want exactly.
> Your g_energy command does exponential averaging, that happens
> on the printed data points. So there g_analyze or any program will do fine.
> For the original data g_energy gives the exact standard deviation
> over all MD steps, called RMSD.
>
> But do you really want the standard deviation, or do you want
> a standard error estimate?
>
> Berk
>
> Date: Fri, 28 Aug 2009 09:30:37 -0300
> From: fabrac...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: g_energy and g_analyze give different averages
>
> Is there a correct way to obtain the standard deviation for these data
> sets?
>
>
>
>
> >
>
> > Ragnarok sdf wrote:
>
> > > When analysing FEP simulations. After running g_energy -f fep000.edr
> -f2
>
> > > fep_000-005.edr for obtaining the dF = -kT ln < exp(-(EB-EA)/kT) >A I
>
> > tried
>
> > > to obtain the standard deviation for this ensemble average using
>
> > g_analyze
>
> > > -f runavg.xvg, but I've noticed that the average values are quite
>
> > different
>
> > >
>
> > >
>
> > g_energy takes all values during your simulation into account, g_analyze
>
> > only the printed datapoints.
>
> >
>
> >
>
>
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[gmx-users] question

[delara aghaie]

--- On Fri, 8/28/09, delara aghaie  wrote:


From: delara aghaie 
Subject: [gmx-users] question
To: gmx-users@gromacs.org
Date: Friday, August 28, 2009, 2:17 AM







Dear Gromaxs users
I want to plot a graph from a remote computer. My operating system is windows 
Vista. I connect to Imperial college in London via VPN connection. There I do 
the simulations using gromacs. Now I want to plot for example the density.xvg 
using gnuplot, but I get this error:X connection to localhost:18.0 broken 
(explicit kill or server shutdown).
 
I should mention that I was able to plot my graphs last week. Now nothing has 
changed but I get this error.
I have putty, and Xming installed on my windows.
Thanks for your guiedence
Delara
 

-Inline Attachment Follows-


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[gmx-users] SIMULATION OF GOLD NANOPARTICLES

[chris . neale]

No information on what you requested, but I do have some tips on how  
to get help from a mailing list. Please understand that I'm sending  
this only to try to help you.


Don't use all caps. Don't double post, we saw the first one. Show us  
that you have done some work and, if possible, approach the list with  
a question that is more well defined. And just in case, don't send a  
personal mail to somebody on this list asking for advice since the  
list is the place to do that.


Chris.

-- original message --

From:  T? 
Subject: [gmx-users] SIMULATION OF GOLD NANOPARTICLES
To: 
Message-ID: <4c581b47098d4bd489c3a2e734841...@laser7>
Content-Type: text/plain; charset="iso-8859-7"


Hi GROMACS users

Does anyone have any information on the simulation of gold  
nanoparticles with GROMACS?


Thank you in advance

George

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[gmx-users] multiple T-Coupling groups

[simon sangma]

Hi,
I used the followng command and encountered an error. Can someone please
offer a solution.
grompp -f grompp.mdp -n index.ndx -p topl.top -c conf.gro -o water.tpr
   :-)  G  R  O  M  A  C  S  (-:
Green Red Orange Magenta Azure Cyan Skyblue

:-)  VERSION 4.0.4  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

:-)  grompp  (-:

Option Filename  Type Description

  -f grompp.mdp  Input, Opt!  grompp input file with MD parameters
 -po  mdout.mdp  Output   grompp input file with MD parameters
  -c   conf.gro  InputStructure file: gro g96 pdb tpr tpb tpa
  -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
 -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
  -n  index.ndx  Input, Opt!  Index file
  -p  topol.top  InputTopology file
 -pp  processed.top  Output, Opt. Topology file
  -o  water.tpr  Output   Run input file: tpr tpb tpa
  -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e   ener.edr  Input, Opt.  Energy file: edr ene

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint0   Set the nicelevel
-[no]v   bool   yes Be loud and noisy
-timereal   -1  Take frame at or first after this time.
-[no]rmvsbds bool   yes Remove constant bonded interactions with virtual
sites
-maxwarn int0   Number of allowed warnings during input
processing
-[no]zerobool   no  Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum   bool   yes Renumber atomtypes and minimize number of
atomtypes

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Ignoring obsolete mdp entry 'domain-decomposition'
Replacing old mdp entry 'unconstrained-start' by 'continuation'

WARNING 1 [file grompp.mdp, line unknown]:
  Unknown or double left-hand 'zero-temp_time' in parameter file


checking input for internal consistency...

WARNING 2 [file grompp.mdp, line unknown]:
  epsilon_r = 0 and epsilon_rf = 1 with reaction field, assuming old format
  and exchanging epsilon_r and epsilon_rf

processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxnb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxbon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Generated 1284 of the 1485 non-bonded parameter combinations
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...

---
Program grompp, VERSION 4.0.4
Source code file: readir.c, line: 1058

Fatal error:
Atom 1 in multiple T-Coupling groups (1 and 2)
---

"Wild Pointers Couldn't Drag Me Away" (K.A. Feenstra)
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Re: [gmx-users] 43A1-S3 FF

[Justin A. Lemkul]

lammps lammps wrote:

Dear gmx developer,

I have read the paper/ " An Improved United Atom Force Field for 
Simulation of Mixed Lipid Bilayers "  J. Phys. Chem. B 2748 2009, 113, 
2748–2763/


Is the new force field (43A1-S3) can instead of the FF of Berger et al. 
for lipid simulations?   When will it be incorporated in the Gromacs 
package?




All necessary files are available for download at the site listed in the paper.

-Justin


Thanks in advance.

--
wende




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--


Justin A. Lemkul
Ph.D. Candidate
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


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[gmx-users] 43A1-S3 FF

[lammps lammps]

Dear gmx developer,

I have read the paper* " An Improved United Atom Force Field for Simulation
of Mixed Lipid Bilayers "  J. Phys. Chem. B 2748 2009, 113, 2748–2763*

Is the new force field (43A1-S3) can instead of the FF of Berger et al. for
lipid simulations?   When will it be incorporated in the Gromacs package?

Thanks in advance.

-- 
wende
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[gmx-users] SIMULATION OF GOLD NANOPARTICLES

[Γεώργιος Tσιγαρίδας]

Hi GROMACS users

Does anyone have any information on the simulation of gold nanoparticles with 
GROMACS?

Thank you in advance

George

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[gmx-users] double precision

[abhijit kayal]

Hi,
I am going to do the normal mode analysis of 1OMB.pdb.For this purpose I
have to run the GROMACS in double precision .For this i went through the
manual and made necessart changes in .mdp file.But when I gave grompp_d it
showed like this
[abhi...@scfbioserver 1omb]$ grompp_d -v -f em.mdp -c b4em.gro -o em.tpr -p
1OMB.top
-bash: grompp_d: command not found.
 I am using GROMACS 4.0.4 version .So my question is why it
showed like this.

Thank you

Abhijit Kayal

IIT Delhi
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RE: [gmx-users] Re: g_energy and g_analyze give different averages

[Berk Hess]

I don't understand what you want exactly.
Your g_energy command does exponential averaging, that happens
on the printed data points. So there g_analyze or any program will do fine.
For the original data g_energy gives the exact standard deviation
over all MD steps, called RMSD.

But do you really want the standard deviation, or do you want
a standard error estimate?

Berk

Date: Fri, 28 Aug 2009 09:30:37 -0300
From: fabrac...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: g_energy and g_analyze give different averages

Is there a correct way to obtain the standard deviation for these data sets?
 



>

> Ragnarok sdf wrote:

> > When analysing FEP simulations. After running g_energy -f fep000.edr -f2

> > fep_000-005.edr for obtaining the dF = -kT ln < exp(-(EB-EA)/kT) >A I

> tried

> > to obtain the standard deviation for this ensemble average using

> g_analyze

> > -f runavg.xvg, but I've noticed that the average values are quite

> different

> >

> >

> g_energy takes all values during your simulation into account, g_analyze

> only the printed datapoints.

>

>





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[gmx-users] SIMULATION OF GOLD NANOPARTICLES

[Γεώργιος Tσιγαρίδας]

Hi GROMACS users

Does anyone have any information on the simulation of gold nanoparticles with 
GROMACS?

Thank you in advance

George

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[gmx-users] Re: g_energy and g_analyze give different averages

[Ragnarok sdf]

Is there a correct way to obtain the standard deviation for these data sets?


> >
> > Ragnarok sdf wrote:
> > > When analysing FEP simulations. After running g_energy -f fep000.edr
> -f2
> > > fep_000-005.edr for obtaining the dF = -kT ln < exp(-(EB-EA)/kT) >A I
> > tried
> > > to obtain the standard deviation for this ensemble average using
> > g_analyze
> > > -f runavg.xvg, but I've noticed that the average values are quite
> > different
> > >
> > >
> > g_energy takes all values during your simulation into account, g_analyze
> > only the printed datapoints.
> >
> >
>
>
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Re: [gmx-users] LINCS

[teklebrh]

Hi Justin,

"There is something physically unrealistic about your model"

You are right!

The main problem I found out is that some of the structures in my  
Solution broke down..


I used ...

genbox -cp .grob -nmol 20 -ci insert.gro -cs spc216.gro XXX.top  
-XX.gro


To generate multiple structures in a box. However, it creates overlap  
and my orginal structures broke down. I checked the structures!


Can you please let me how to generate multiple structures in a fixed  
box at random or packed in a solutio (e.g water)


Thank you for you help

Robella











Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

Hi Justin,

I tried to run full MD after energy minimization in both vacuo and  
water... went good but I got this ERROR once I try to run full MD.


Can you please help.


There is something physically unrealistic about your model.  That's  
the case whenever you see a LINCS warning.  Without a more complete  
description of what you've done (minimization and equilibration  
protocol, initial construction of the model, etc) and the details of  
your simulation parameters, there's nothing more anyone can really  
say beyond a guess.


It appears that the wiki is down at the moment, but these pages have  
useful information (when the site comes back up):


http://oldwiki.gromacs.org/index.php/blowing_up
http://oldwiki.gromacs.org/index.php/Errors

And since LINCS errors have been posted thousands of times to the  
list, the archive should have some useful advice as well, so search  
here:


http://oldwww.gromacs.org/swish-e/search/search2.php

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
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


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Re: [gmx-users] Re: wierd behavior of mdrun

[Mark Abraham]

Vitaly V. Chaban wrote:

Then I believe you have problems with MPI.

Before I experienced something alike on our old system - serial
version worked OK but parallel one failed. The same issue was with
CPMD by the way. Another programs worked fine. I didn't correct that
problem...

On Thu, Aug 27, 2009 at 7:14 PM, Paymon Pirzadeh wrote:

Yes,
it works when it is run on one processor interactively!


That's fine, but it doesn't mean the problem is with the parallelism, as 
Vitaly suggests. If your cluster filesystem isn't configured properly, 
you will observe these symptoms. Since the submission script was the 
same, MPI worked previously, so isn't likely to be the problem...


Mark


On Thu, 2009-08-27 at 09:23 +0300, Vitaly V. Chaban wrote:

I made a .tpr file for my md run without any problems (using the bottom
mdp file). My job submission script is also the same thing I used for
other jobs which had no problems. But now when I submit this .tpr file,
only an empty log file is generated! The qstat of the cluster shows that
the job is running, also the processors are 100% engaged while I have no
outputs!

A standard guess: what about trying to run the single-processor job on
the same cluster? Does it run OK?



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[gmx-users] grompp crashes when submitted to the cluster

[Itamar Kass]

Hi,

I have compiled gromacs 4.0.5 on our mac cluster (64bit) using openmpi  
1.3.3 and gcc 4.2.1.


No my problem is grompp. When I manually run grompp it runs smoothly,  
but when I run it as part of a job to our cluster it crashes:


/var/spool/torque/mom_priv/jobs/ ... .SC: line 27: 91546 Segmentation  
fault  grompp


Any idea?

Cheers,
Itamar

---

 "In theory, there is no difference between theory and practice. But,  
in practice, there is." - Jan L.A. van de Snepscheut


===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@med.monash.edu.au


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RE: [gmx-users] wierd behavior of mdrun

[Dallas B. Warren]

How is it that the date and time is wrong?  It is simply telling you
that the simulation will be completed on Sep 16, using the time on the
computer that the program is running on.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology 
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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Re: [gmx-users] error in ATOM2CG.awk script

[sunny mishra]

Yeah I agree wiht you but I tested another protein as well 1BL8 to check if
there was a problem specifically in 1K4C. Even after testing 1BL8 it gives
me the same error. What do you think?

On Thu, Aug 27, 2009 at 4:11 PM, Justin A. Lemkul  wrote:

>
>
> sunny mishra wrote:
>
>> Dear all,
>>
>> I was earlier facing problem regarding the mismatch of atoms in .top and
>> .gro file and then after useful discussion here I figured out that some
>> atoms were missing in my cg.pdb file and that problem is because of the
>> OLDER atom2cg.awk script which MARTINI folks have in their website. When I
>> was using the earlier version of atom2cg.awk script I had 776 atoms in my
>> .gro file and 804 atoms in .itp file and thats why .top and .gro were not
>> matching but again the same problem raised even after using the new
>> atom2cg.awk script which they sent me but it included some ILE residues and
>> now I have 784 atoms in .gro file and 804 atoms in .itp file
>>
>>
> As I recall, the root problem was that the original .pdb file from the RCSB
> had missing atoms that you had not properly modeled back in.
>
>  I pretty much now know how to fix the script but I am confused in some of
>> the things like:
>>
>> 1) In the cleaned.pdb file of my protein the ARG residue in the
>> atom2cg.awk script takes only CA, CG and NE with BN0, SC1, and SC2. If I
>> want to include other atoms as well like NH1, NH2, CZ, CD etc what should I
>> print for these atoms (either BN0, SC1, or SC2). As a matter of fact I don't
>> know what do SC1, BN0, SC2 mean?
>>
>
> Hence the point of CG.  You don't account for every single atom that was in
> the atomistic structure.  BN0 = backbone particle, SC1 and SC2 are side
> chain particles that will be given specific attributes in the topology.
>
> You should probably refer to the MARTINI publications for a more clear
> understanding of how the force field was conceived and how it should be
> used.
>
> -Justin
>
>  So, i don't know while adding other atoms for ARG residue what should I
>> print for them and I searched in the martini website but could not find
>> anything. Please let me know if you got my problem.
>>
>> Thanks,
>>
>> Sunny
>>
>>
>>
>> 
>>
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>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> 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
>
> 
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Re: [gmx-users] error in ATOM2CG.awk script

[XAvier Periole]

On Aug 27, 2009, at 2:51 PM, sunny mishra wrote:


Dear all,

I was earlier facing problem regarding the mismatch of atoms in .top  
and .gro file and then after useful discussion here I figured out  
that some atoms were missing in my cg.pdb file and that problem is  
because of the OLDER atom2cg.awk script which MARTINI folks have in  
their website. When I was using the earlier version of atom2cg.awk  
script I had 776 atoms in my .gro file and 804 atoms in .itp file  
and thats why .top and .gro were not matching but again the same  
problem raised even after using the new atom2cg.awk script which  
they sent me but it included some ILE residues and now I have 784  
atoms in .gro file and 804 atoms in .itp file


I pretty much now know how to fix the script but I am confused in  
some of the things like:

Could you explain what was wrong and how you've fixed it.
Who gave you the new file?
1) In the cleaned.pdb file of my protein the ARG residue in the  
atom2cg.awk script takes only CA, CG and NE with BN0, SC1, and SC2.  
If I want to include other atoms as well like NH1, NH2, CZ, CD etc  
what should I print for these atoms (either BN0, SC1, or SC2). As a  
matter of fact I don't know what do SC1, BN0, SC2 mean?
I am not sure what you actually intent to do but adding atoms to use  
on the CG level does not sound

like something you'll want to do.
SC1/SC2 are the names for the side chains beads and BN0 is for the  
backbone bead with the

type N0.


So, i don't know while adding other atoms for ARG residue what  
should I print for them and I searched in the martini website but  
could not find anything. Please let me know if you got my problem.


Thanks,

Sunny


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[gmx-users] question

[delara aghaie]

Dear Gromaxs users
I want to plot a graph from a remote computer. My operating system is windows 
Vista. I connect to Imperial college in London via VPN connection. There I do 
the simulations using gromacs. Now I want to plot for example the density.xvg 
using gnuplot, but I get this error:X connection to localhost:18.0 broken 
(explicit kill or server shutdown).
 
I should mention that I was able to plot my graphs last week. Now nothing has 
changed but I get this error.
I have putty, and Xming installed on my windows.
Thanks for your guiedence
Delara
 


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[gmx-users] grompp crashes when submitted to the cluster

[Itamar Kass]

Hi,

I have compiled gromacs 4.0.5 on our mac cluster (64bit) using openmpi
1.3.3 and gcc 4.2.1.

No my problem is grompp. When I manually run grompp it runs smoothly,
but when I run it as part of a job to our cluster it crashes:

/var/spool/torque/mom_priv/jobs/ ... .SC: line 27: 91546 Segmentation
fault  grompp

Any idea?

Cheers,
Itamar

---

 "In theory, there is no difference between theory and practice. But,
in practice, there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@med.monash.edu.au

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Re: [gmx-users] wierd behavior of mdrun

[Mark Abraham]

Paymon Pirzadeh wrote:

One more point:
when I run the job interactively, although it works but date and time
are wrong!

step 0
step 100, will finish Wed Sep 16 16:16:00 2009
step 200, will finish Wed Sep 16 14:32:34 2009
step 300, will finish Wed Sep 16 13:57:51 2009
step 400, will finish Wed Sep 16 11:35:46 2009
step 500, will finish Wed Sep 16 11:50:12 2009
step 600, will finish Wed Sep 16 10:36:38 2009
step 700, will finish Wed Sep 16 09:44:04 2009
step 800, will finish Wed Sep 16 10:07:02 2009
step 900, will finish Wed Sep 16 09:29:25 2009
step 1000, will finish Wed Sep 16 08:59:19 2009
step 1100, will finish Wed Sep 16 09:20:06 2009
step 1200, will finish Wed Sep 16 08:55:47 2009
step 1300, will finish Wed Sep 16 09:13:38 2009
step 1400, will finish Wed Sep 16 08:53:15 2009

Is it a cluster related or GROMACS related issue? Is it important at
all?


That's just an estimate based on the elapsed wall time. If the source of 
elapsed wall time is unreliable or wrong, or the sample of wall time is 
too short, then the estimate will be wrong or vary widely accordingly.


This prediction should stabilize over the course of the run.

Mark
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