date:20130212

[gmx-users] Re: Reference structure for PCA.

2013-02-12 Thread vivek modi

>
>
> Message: 1
> Date: Sun, 10 Feb 2013 21:32:15 + (WET)
> From: bapti...@itqb.unl.pt
> Subject: Re: [gmx-users] Reference structure for PCA.
> To: Discussion list for GROMACS users 
> Message-ID: 
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>

Hello Antonio,

Thank you very much for the reply. I have gone through the paper you
mentioned. The central structure seems to be a good choice for the
reference structure.


Regards,

-Vivek.


>
> Hi Vivek,
>
> There are two distinct steps involved: (1) the fit of your trajectory to a
> reference structure, which corresponds to choose a conformation space; (2)
> the use of the PCA method, which corresponds to find in that space a new
> basis set whose ordered axes sequentially maximize dispersion (hopefully
> capturing the distribution main features with only a few of the new
> coordinates). The two steps just happen to be done by the same program.
> The structure chosen for fitting is related to step 1, while the average
> structure used to compute the covariance matrix is related to step 2 -- as
> already pointed by Tjerk, the two structures are generally not the same.
>
> The aim of the fit is to get rid of the global translation and rotation of
> your protein in the simulation box, trying to place all the sampled
> structures in a single 3D space that reflects "only" the conformational
> differences. But this is necessarily approximate, because the
> superimposition of any pair of structures after the global fit will be
> always worse than you would get by making a pairwise fit of the two. Thus,
> you want to get a final dispersion around the reference as small as
> possible. So, of the two average structures that you tried, you should
> choose the one computed from the last 30 ns (it's not surprising that it
> gives a smaller dispersion, because it refers to the segment you are
> analyzing). Still, using an average structure as a reference is a somewhat
> illusory solution, because that average must itself be obtained after
> fitting the trajectory to some reference... In a study of a small flexible
> peptide (where the choice of reference may have drastic effects), we found
> that a good reference seems to be the "central structure" of your sample,
> defined as the one that, when taken as a reference, leads to the lowest
> overall dispersion (http://dx.doi.org/10.1021/jp902991u). The article
> discusses the issues pointed above, so you may want to give it a look.
>
> You can also avoid the need of a reference by choosing a different
> conformation space for PCA, a popular alternative being the phi and psi
> dihedrals (look in the manual). Note that this dihedral space is a bit
> different from the more usual one discussed above, each reflecting a
> different kind of conformational proximity (this is also discussed in the
> article). It's up to you to decide which one better suits your problem.
>
> Hope this helps.
> Cheers,
> Antonio
>
> Thank you very much for your reply Tsjerk.
I understand that the two reference structures are different. I had a query
because I found the method is very sensitive to the choice of the reference
structure for fitting. Most of the publications either do not mention the
reference structure. Only in few papers I found initial structure for
fitting. But the method gives different  results if initial structure is
used; or average from complete trajectory;  or average over a certain time
window is used as the structure for reference.
The average was calculated using the following command:

g_rmsf -f *.xtc -s *.tpr -ox average70-100ns.pdb -b 7 -e 10



Regards,

-Vivek.



> On Sat, 9 Feb 2013, Tsjerk Wassenaar wrote:
>
> > Hi,
> >
> > The commands would certainly help, including the commands for getting the
> > reference structure. Do note that the reference is the reference for
> > fitting, which is 'external', i.e. provided by the user. This is not the
> > same as the structure used to calculate the deviations, which is the
> > average structure of the frames selected.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Sat, Feb 9, 2013 at 7:06 PM, bipin singh 
> wrote:
> >
> >> Hi vivek,
> >>
> >> I have few questions related to your query:
> >>
> >> During covariance matrix calculation, g_covar by default takes average
> >> structure of the trajectory as a reference structure then why you are
> >> giving it average structure of your trajectory (0-100ns) manually.
> >> Moreover without looking at your commands which you have used, it would
> be
> >> difficult for anyone that why are you getting these surprising results.
> >> On Thu, Feb 7, 2013 at 1:26 PM, vivek modi 
> >> wrote:
> >>
> >>> Hello,
> >>>
> >>> I have troubled you with a similar question before also, but I guess I
> >> need
> >>> some more clarification. My question is about the reference structure
> in
> >>> PCA analysis.
> >>> I have 100ns long protein simulation which I want to analyze using PCA.
> >> The
> >>> RMSD shows fluctuations upto

[gmx-users] Re: Problem with dihedral restraint in gromacs 4.6

2013-02-12 Thread Landraille

Last question (I hope).

How can I choose the force constant?

Indeed for the version 4.5, the force constant is defined by the  
option dihre_fc in the mdp input file. After this force is multiply by  
kfac contained in the dihedral_sections in the topology file

Now this option is obsolete. The force constant is defined by kfac in  
gromacs4.6 ? If yes, kfac has now a unit. In kJ.mol-1.rad-2 ?

Thank you 



--
View this message in context: 
http://gromacs.5086.n6.nabble.com/Problem-with-dihedral-restraint-in-gromacs-4-6-tp5005302p5005443.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: Reference structure for PCA.

2013-02-12 Thread Tsjerk Wassenaar

Hi Vivek,

If you use the g_covar option -ref, you not only use the reference
structure for fitting, you use it for calculating the deviations. Your
covariance matrix is built as:

S = 1/N sum (x - ref) (x - ref)'

If you leave out the option -ref then the average structure will be
used for the covariance matrix, which is what you (should) want. In
that case the reference structure is only used for fitting. You might
want to redo your calculations to check the effect of fitting.

Cheers,

Tsjerk

On Tue, Feb 12, 2013 at 9:02 AM, vivek modi  wrote:
>>
>>
>> Message: 1
>> Date: Sun, 10 Feb 2013 21:32:15 + (WET)
>> From: bapti...@itqb.unl.pt
>> Subject: Re: [gmx-users] Reference structure for PCA.
>> To: Discussion list for GROMACS users 
>> Message-ID: 
>> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>>
>
> Hello Antonio,
>
> Thank you very much for the reply. I have gone through the paper you
> mentioned. The central structure seems to be a good choice for the
> reference structure.
>
>
> Regards,
>
> -Vivek.
>
>
>>
>> Hi Vivek,
>>
>> There are two distinct steps involved: (1) the fit of your trajectory to a
>> reference structure, which corresponds to choose a conformation space; (2)
>> the use of the PCA method, which corresponds to find in that space a new
>> basis set whose ordered axes sequentially maximize dispersion (hopefully
>> capturing the distribution main features with only a few of the new
>> coordinates). The two steps just happen to be done by the same program.
>> The structure chosen for fitting is related to step 1, while the average
>> structure used to compute the covariance matrix is related to step 2 -- as
>> already pointed by Tjerk, the two structures are generally not the same.
>>
>> The aim of the fit is to get rid of the global translation and rotation of
>> your protein in the simulation box, trying to place all the sampled
>> structures in a single 3D space that reflects "only" the conformational
>> differences. But this is necessarily approximate, because the
>> superimposition of any pair of structures after the global fit will be
>> always worse than you would get by making a pairwise fit of the two. Thus,
>> you want to get a final dispersion around the reference as small as
>> possible. So, of the two average structures that you tried, you should
>> choose the one computed from the last 30 ns (it's not surprising that it
>> gives a smaller dispersion, because it refers to the segment you are
>> analyzing). Still, using an average structure as a reference is a somewhat
>> illusory solution, because that average must itself be obtained after
>> fitting the trajectory to some reference... In a study of a small flexible
>> peptide (where the choice of reference may have drastic effects), we found
>> that a good reference seems to be the "central structure" of your sample,
>> defined as the one that, when taken as a reference, leads to the lowest
>> overall dispersion (http://dx.doi.org/10.1021/jp902991u). The article
>> discusses the issues pointed above, so you may want to give it a look.
>>
>> You can also avoid the need of a reference by choosing a different
>> conformation space for PCA, a popular alternative being the phi and psi
>> dihedrals (look in the manual). Note that this dihedral space is a bit
>> different from the more usual one discussed above, each reflecting a
>> different kind of conformational proximity (this is also discussed in the
>> article). It's up to you to decide which one better suits your problem.
>>
>> Hope this helps.
>> Cheers,
>> Antonio
>>
>> Thank you very much for your reply Tsjerk.
> I understand that the two reference structures are different. I had a query
> because I found the method is very sensitive to the choice of the reference
> structure for fitting. Most of the publications either do not mention the
> reference structure. Only in few papers I found initial structure for
> fitting. But the method gives different  results if initial structure is
> used; or average from complete trajectory;  or average over a certain time
> window is used as the structure for reference.
> The average was calculated using the following command:
>
> g_rmsf -f *.xtc -s *.tpr -ox average70-100ns.pdb -b 7 -e 10
>
>
>
> Regards,
>
> -Vivek.
>
>
>
>> On Sat, 9 Feb 2013, Tsjerk Wassenaar wrote:
>>
>> > Hi,
>> >
>> > The commands would certainly help, including the commands for getting the
>> > reference structure. Do note that the reference is the reference for
>> > fitting, which is 'external', i.e. provided by the user. This is not the
>> > same as the structure used to calculate the deviations, which is the
>> > average structure of the frames selected.
>> >
>> > Cheers,
>> >
>> > Tsjerk
>> >
>> > On Sat, Feb 9, 2013 at 7:06 PM, bipin singh 
>> wrote:
>> >
>> >> Hi vivek,
>> >>
>> >> I have few questions related to your query:
>> >>
>> >> During covariance matrix calculation, g_covar by default takes average
>> >> structure of the

[gmx-users] additional bond description (isopeptide bond) between two chains

2013-02-12 Thread durdagis

Hello all,

I have an isopeptide bond (between Lys site chain and carboxyl terminal of
Gly) in my system and I defined this with specbond.dat and additional
residue types and I edited .rtp files using Amber ff. Although I have this
bond at the beginning (before pdb2gmx), it looks I need to add additional
description for this bond (between two different chains) at the topology
definition. How can I define it? (please see the picture, this is after
energy min.)

serdar

 



--
View this message in context: 
http://gromacs.5086.n6.nabble.com/additional-bond-description-isopeptide-bond-between-two-chains-tp5005445.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Removing errors related to missing dihedrals.

2013-02-12 Thread Abhishek Acharya

Hello Justin.
Help would really be appreciated. And yes you are correct and i
thought the same. Initially I tried using opls_345B but it didn't
work. In fact if I use opls_345B it gives me an additional error.
Anyhow here are the relevant files.
topology file:
 #   [atoms]
15  ;   nr   type  resnr residue  atom   cgnr charge
mass  typeBchargeB  massB
16   1   opls_445  1GDP  P  0  1.2596
30.97376
17   2   opls_446  1GDP O2  0 -0.9034
15.99940
18   3   opls_446  1GDP O2  0 -0.9070
15.99940
19   4   opls_446  1GDP O2  0 -0.9275
15.99940
20   5   opls_441  1GDP O2  0 -0.5156
15.99940
21   6   opls_440  1GDP  P  0  1.2391
30.97376
22   7   opls_441  1GDP O2  0 -0.8867
15.99940
23   8   opls_441  1GDP O2  0 -0.8450
15.99940
24   9   opls_442  1GDP OS  0  0.4846
15.99940
25  10   opls_443  1GDP CT  1  0.0706
12.01100
26  11   opls_140  1GDP HC  1  0.0827
1.00800
27  12   opls_140  1GDP HC  1  0.0827
1.00800
28  13   opls_183  1GDP CT  2  0.0348
12.01100
29  14   opls_185  1GDP HC  2  0.0538
1.00800
30  15   opls_180  1GDP OS  2 -0.4621
15.99940
31  16   opls_158  1GDP CT  3  0.2388
12.01100
32  17   opls_156  1GDP HC  3  0.1674
1.00800
33  18   opls_154  1GDP OH  3 -0.7755
15.99940
34  19   opls_155  1GDP HO  3  0.4336
1.00800
35  20   opls_158  1GDP CT  4  0.2713
12.01100
36  21   opls_156  1GDP HC  4  0.0890
1.00800
37  22   opls_154  1GDP OH  4 -0.7534
15.99940
38  23   opls_155  1GDP HO  4  0.4404
1.00800
39  24   opls_137  1GDP CT  5 -0.0774
12.01100
40  25   opls_140  1GDP HC  5  0.0594
1.00800
41  26   opls_354  1GDP NA  6  0.1656
14.00670
42  27   opls_353  1GDP CK  7  0.1470
12.01100
43  28   opls_359  1GDP H5  7  0.2255
1.00800
44  29   opls_352  1GDP NB  8 -0.5913
14.00670
45  30   opls_365  1GDP CB  9  0.1189
12.01100
46  31   opls_366  1GDP  C 10  0.5578
12.01100
47  32   opls_370  1GDP  O 10 -0.6203   14.00670
48  33   opls_361  1GDP NA 11 -0.5509
14.00670
49  34   opls_367  1GDP  H 11  0.3354
1.00800
50  35   opls_362  1GDP CA 12  0.7061
12.01100
51  36   opls_368  1GDP N2 13 -0.9532
14.00670
52  37   opls_369  1GDP  H 13  0.3790
1.00800
53  38   opls_369  1GDP  H 13  0.3790
1.00800
54  39   opls_363  1GDP NC 14 -0.5526
14.00670
55  40   opls_364  1GDP CB 15  0.1142   12.01100

225 [ dihedrals ]
226 ;  aiajakal funct
22725242627 3
22825242640 3
22924262728 3
23024262729 3
23136353940 3
23221202223 3
23321202425 3
23421202426 3
23522202425 3
23622202426 3
23718162021 3
23818162022 3
23918162024 3
24017162021 3
24117162022 3
24217162024 3
24314131524 3
24414131618 3
24514131617 3
24614131620 3
24715131618 3
24815131617 3
24915131620 3
25013152425 3
251   13152426 3
25230313335 3
25312101314 3
25412101315 3
25512101316 3
25611101314 3
25711101315 3
25811101316 3
25932313335 3
26031333536 3
26131333539 3
26228272930 3
26327293031 3
26427293040 3
26534333536 3
26634333539 3
267 5 6 910 3

The output:

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations

ERROR 1 [file p2gout_GDP.itp, line 234]:
  No default Ryckaert-Bell. types


ERROR 2 [file p2gout_GDP.itp, line 236]:

Re: [gmx-users] Re: Reference structure for PCA.

2013-02-12 Thread Ahmet yıldırım

Hi,

S = 1/N sum (x - ref) (x - ref)'

or

S = 1/(N-1) sum (x - ref) (x - ref)'

N: the number of frames

Which one is right?

2013/2/12 Tsjerk Wassenaar 

> Hi Vivek,
>
> If you use the g_covar option -ref, you not only use the reference
> structure for fitting, you use it for calculating the deviations. Your
> covariance matrix is built as:
>
> S = 1/N sum (x - ref) (x - ref)'
>
> If you leave out the option -ref then the average structure will be
> used for the covariance matrix, which is what you (should) want. In
> that case the reference structure is only used for fitting. You might
> want to redo your calculations to check the effect of fitting.
>
> Cheers,
>
> Tsjerk
>
> On Tue, Feb 12, 2013 at 9:02 AM, vivek modi 
> wrote:
> >>
> >>
> >> Message: 1
> >> Date: Sun, 10 Feb 2013 21:32:15 + (WET)
> >> From: bapti...@itqb.unl.pt
> >> Subject: Re: [gmx-users] Reference structure for PCA.
> >> To: Discussion list for GROMACS users 
> >> Message-ID: 
> >> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
> >>
> >
> > Hello Antonio,
> >
> > Thank you very much for the reply. I have gone through the paper you
> > mentioned. The central structure seems to be a good choice for the
> > reference structure.
> >
> >
> > Regards,
> >
> > -Vivek.
> >
> >
> >>
> >> Hi Vivek,
> >>
> >> There are two distinct steps involved: (1) the fit of your trajectory
> to a
> >> reference structure, which corresponds to choose a conformation space;
> (2)
> >> the use of the PCA method, which corresponds to find in that space a new
> >> basis set whose ordered axes sequentially maximize dispersion (hopefully
> >> capturing the distribution main features with only a few of the new
> >> coordinates). The two steps just happen to be done by the same program.
> >> The structure chosen for fitting is related to step 1, while the average
> >> structure used to compute the covariance matrix is related to step 2 --
> as
> >> already pointed by Tjerk, the two structures are generally not the same.
> >>
> >> The aim of the fit is to get rid of the global translation and rotation
> of
> >> your protein in the simulation box, trying to place all the sampled
> >> structures in a single 3D space that reflects "only" the conformational
> >> differences. But this is necessarily approximate, because the
> >> superimposition of any pair of structures after the global fit will be
> >> always worse than you would get by making a pairwise fit of the two.
> Thus,
> >> you want to get a final dispersion around the reference as small as
> >> possible. So, of the two average structures that you tried, you should
> >> choose the one computed from the last 30 ns (it's not surprising that it
> >> gives a smaller dispersion, because it refers to the segment you are
> >> analyzing). Still, using an average structure as a reference is a
> somewhat
> >> illusory solution, because that average must itself be obtained after
> >> fitting the trajectory to some reference... In a study of a small
> flexible
> >> peptide (where the choice of reference may have drastic effects), we
> found
> >> that a good reference seems to be the "central structure" of your
> sample,
> >> defined as the one that, when taken as a reference, leads to the lowest
> >> overall dispersion (http://dx.doi.org/10.1021/jp902991u). The article
> >> discusses the issues pointed above, so you may want to give it a look.
> >>
> >> You can also avoid the need of a reference by choosing a different
> >> conformation space for PCA, a popular alternative being the phi and psi
> >> dihedrals (look in the manual). Note that this dihedral space is a bit
> >> different from the more usual one discussed above, each reflecting a
> >> different kind of conformational proximity (this is also discussed in
> the
> >> article). It's up to you to decide which one better suits your problem.
> >>
> >> Hope this helps.
> >> Cheers,
> >> Antonio
> >>
> >> Thank you very much for your reply Tsjerk.
> > I understand that the two reference structures are different. I had a
> query
> > because I found the method is very sensitive to the choice of the
> reference
> > structure for fitting. Most of the publications either do not mention the
> > reference structure. Only in few papers I found initial structure for
> > fitting. But the method gives different  results if initial structure is
> > used; or average from complete trajectory;  or average over a certain
> time
> > window is used as the structure for reference.
> > The average was calculated using the following command:
> >
> > g_rmsf -f *.xtc -s *.tpr -ox average70-100ns.pdb -b 7 -e 10
> >
> >
> >
> > Regards,
> >
> > -Vivek.
> >
> >
> >
> >> On Sat, 9 Feb 2013, Tsjerk Wassenaar wrote:
> >>
> >> > Hi,
> >> >
> >> > The commands would certainly help, including the commands for getting
> the
> >> > reference structure. Do note that the reference is the reference for
> >> > fitting, which is 'external', i.e. provided by the user. This is not
> the

Re: [gmx-users] Removing errors related to missing dihedrals.

2013-02-12 Thread Justin Lemkul




On 2/12/13 6:19 AM, Abhishek Acharya wrote:

Hello Justin.
Help would really be appreciated. And yes you are correct and i
thought the same. Initially I tried using opls_345B but it didn't
work. In fact if I use opls_345B it gives me an additional error.
Anyhow here are the relevant files.
topology file:
  #   [atoms]
15  ;   nr   type  resnr residue  atom   cgnr charge
mass  typeBchargeB  massB
16   1   opls_445  1GDP  P  0  1.2596
30.97376
17   2   opls_446  1GDP O2  0 -0.9034
15.99940
18   3   opls_446  1GDP O2  0 -0.9070
15.99940
19   4   opls_446  1GDP O2  0 -0.9275
15.99940
20   5   opls_441  1GDP O2  0 -0.5156
15.99940
21   6   opls_440  1GDP  P  0  1.2391
30.97376
22   7   opls_441  1GDP O2  0 -0.8867
15.99940
23   8   opls_441  1GDP O2  0 -0.8450
15.99940
24   9   opls_442  1GDP OS  0  0.4846
15.99940
25  10   opls_443  1GDP CT  1  0.0706
12.01100
26  11   opls_140  1GDP HC  1  0.0827
1.00800
27  12   opls_140  1GDP HC  1  0.0827
1.00800
28  13   opls_183  1GDP CT  2  0.0348
12.01100
29  14   opls_185  1GDP HC  2  0.0538
1.00800
30  15   opls_180  1GDP OS  2 -0.4621
15.99940
31  16   opls_158  1GDP CT  3  0.2388
12.01100
32  17   opls_156  1GDP HC  3  0.1674
1.00800
33  18   opls_154  1GDP OH  3 -0.7755
15.99940
34  19   opls_155  1GDP HO  3  0.4336
1.00800
35  20   opls_158  1GDP CT  4  0.2713
12.01100
36  21   opls_156  1GDP HC  4  0.0890
1.00800
37  22   opls_154  1GDP OH  4 -0.7534
15.99940
38  23   opls_155  1GDP HO  4  0.4404
1.00800
39  24   opls_137  1GDP CT  5 -0.0774
12.01100
40  25   opls_140  1GDP HC  5  0.0594
1.00800
41  26   opls_354  1GDP NA  6  0.1656
14.00670
42  27   opls_353  1GDP CK  7  0.1470
12.01100
43  28   opls_359  1GDP H5  7  0.2255
1.00800
44  29   opls_352  1GDP NB  8 -0.5913
14.00670
45  30   opls_365  1GDP CB  9  0.1189
12.01100
46  31   opls_366  1GDP  C 10  0.5578
12.01100
47  32   opls_370  1GDP  O 10 -0.6203   14.00670
48  33   opls_361  1GDP NA 11 -0.5509
14.00670
49  34   opls_367  1GDP  H 11  0.3354
1.00800
50  35   opls_362  1GDP CA 12  0.7061
12.01100
51  36   opls_368  1GDP N2 13 -0.9532
14.00670
52  37   opls_369  1GDP  H 13  0.3790
1.00800
53  38   opls_369  1GDP  H 13  0.3790
1.00800
54  39   opls_363  1GDP NC 14 -0.5526
14.00670
55  40   opls_364  1GDP CB 15  0.1142   12.01100

225 [ dihedrals ]
226 ;  aiajakal funct
22725242627 3
22825242640 3
22924262728 3
23024262729 3
23136353940 3
23221202223 3
23321202425 3
23421202426 3
23522202425 3
23622202426 3
23718162021 3
23818162022 3
23918162024 3
24017162021 3
24117162022 3
24217162024 3
24314131524 3
24414131618 3
24514131617 3
24614131620 3
24715131618 3
24815131617 3
24915131620 3
25013152425 3
251   13152426 3
25230313335 3
25312101314 3
25412101315 3
25512101316 3
25611101314 3
25711101315 3
25811101316 3
25932313335 3
26031333536 3
26131333539 3
26228272930 3
26327293031 3
26427293040 3
26534333536 3
26634333539 3
267 5 6 910 3

The output:

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations



You haven't listed what you've done to try to address these (i.e.,

Re: [gmx-users] additional bond description (isopeptide bond) between two chains

2013-02-12 Thread Justin Lemkul




On 2/12/13 3:30 AM, durdagis wrote:

Hello all,

I have an isopeptide bond (between Lys site chain and carboxyl terminal of
Gly) in my system and I defined this with specbond.dat and additional
residue types and I edited .rtp files using Amber ff. Although I have this
bond at the beginning (before pdb2gmx), it looks I need to add additional
description for this bond (between two different chains) at the topology
definition. How can I define it? (please see the picture, this is after
energy min.)



Visualization programs detect what they think are bonds by heuristic algorithms. 
 Whether or not a bond shows up in a visualization program is irrelevant.  What 
actually matters is whether or not the bond shows up in the topology that 
pdb2gmx created.  Your approach sounds correct, so you should be fine.  Check 
the topology to make sure the bond is there, and use simple Gromacs tools like 
g_dist to ensure the effect of the bond over the course of a test simulation.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Water mediated H-bonds

2013-02-12 Thread Justin Lemkul




On 2/12/13 1:12 AM, neeru sharma wrote:

Dear Gromacs Users,


I have simulated a system of protein-ion complex. As a part of the
analysis, I want to see whether there are any H-bonds or other interactions
between the active site residues and the water surrounding those residues.
I was trying to perform the same using g_hbond program of gromacs, but
could not get any output. I tried with varying the cut off value and as
well specifying the "contact" option to look for the non H-bond
interactions too, that fall within the cut off mentioned.

Can anybody suggest me how to look for the H-bonds between protein residues
and water molecules?



Your question and subject line refer to different things.  Detecting hydrogen 
bonds between protein residues and water is trivial.  Create index groups for 
the residues of interest and select these residues and water as the two groups 
for g_hbond.  Water-mediated hydrogen bonds between residues, however, are far 
more difficult to obtain, but this topic has been covered many times in the list 
archive.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: Reference structure for PCA.

2013-02-12 Thread Tsjerk Wassenaar

Hey Ahmet,

1/(N-1) sum (x-mean)(x-mean)'

is the unbiased estimator of the true (population) covariance matrix,
provided the observations are mutually independent (!)

In most cases, N is quite large, so it doesn't actually matter, and
the eigenvectors and order (not size) of the eigenvalues are invariant
to scaling, so it doesn't actually matter. If the size of the
eigenvalues does matter, you better make sure that there is no
temporal correlation between the frames you use for the analysis.

Cheers,

Tsjerk

On Tue, Feb 12, 2013 at 1:53 PM, Ahmet yıldırım  wrote:
> Hi,
>
> S = 1/N sum (x - ref) (x - ref)'
>
> or
>
> S = 1/(N-1) sum (x - ref) (x - ref)'
>
> N: the number of frames
>
> Which one is right?
>
> 2013/2/12 Tsjerk Wassenaar 
>
>> Hi Vivek,
>>
>> If you use the g_covar option -ref, you not only use the reference
>> structure for fitting, you use it for calculating the deviations. Your
>> covariance matrix is built as:
>>
>> S = 1/N sum (x - ref) (x - ref)'
>>
>> If you leave out the option -ref then the average structure will be
>> used for the covariance matrix, which is what you (should) want. In
>> that case the reference structure is only used for fitting. You might
>> want to redo your calculations to check the effect of fitting.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Tue, Feb 12, 2013 at 9:02 AM, vivek modi 
>> wrote:
>> >>
>> >>
>> >> Message: 1
>> >> Date: Sun, 10 Feb 2013 21:32:15 + (WET)
>> >> From: bapti...@itqb.unl.pt
>> >> Subject: Re: [gmx-users] Reference structure for PCA.
>> >> To: Discussion list for GROMACS users 
>> >> Message-ID: 
>> >> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>> >>
>> >
>> > Hello Antonio,
>> >
>> > Thank you very much for the reply. I have gone through the paper you
>> > mentioned. The central structure seems to be a good choice for the
>> > reference structure.
>> >
>> >
>> > Regards,
>> >
>> > -Vivek.
>> >
>> >
>> >>
>> >> Hi Vivek,
>> >>
>> >> There are two distinct steps involved: (1) the fit of your trajectory
>> to a
>> >> reference structure, which corresponds to choose a conformation space;
>> (2)
>> >> the use of the PCA method, which corresponds to find in that space a new
>> >> basis set whose ordered axes sequentially maximize dispersion (hopefully
>> >> capturing the distribution main features with only a few of the new
>> >> coordinates). The two steps just happen to be done by the same program.
>> >> The structure chosen for fitting is related to step 1, while the average
>> >> structure used to compute the covariance matrix is related to step 2 --
>> as
>> >> already pointed by Tjerk, the two structures are generally not the same.
>> >>
>> >> The aim of the fit is to get rid of the global translation and rotation
>> of
>> >> your protein in the simulation box, trying to place all the sampled
>> >> structures in a single 3D space that reflects "only" the conformational
>> >> differences. But this is necessarily approximate, because the
>> >> superimposition of any pair of structures after the global fit will be
>> >> always worse than you would get by making a pairwise fit of the two.
>> Thus,
>> >> you want to get a final dispersion around the reference as small as
>> >> possible. So, of the two average structures that you tried, you should
>> >> choose the one computed from the last 30 ns (it's not surprising that it
>> >> gives a smaller dispersion, because it refers to the segment you are
>> >> analyzing). Still, using an average structure as a reference is a
>> somewhat
>> >> illusory solution, because that average must itself be obtained after
>> >> fitting the trajectory to some reference... In a study of a small
>> flexible
>> >> peptide (where the choice of reference may have drastic effects), we
>> found
>> >> that a good reference seems to be the "central structure" of your
>> sample,
>> >> defined as the one that, when taken as a reference, leads to the lowest
>> >> overall dispersion (http://dx.doi.org/10.1021/jp902991u). The article
>> >> discusses the issues pointed above, so you may want to give it a look.
>> >>
>> >> You can also avoid the need of a reference by choosing a different
>> >> conformation space for PCA, a popular alternative being the phi and psi
>> >> dihedrals (look in the manual). Note that this dihedral space is a bit
>> >> different from the more usual one discussed above, each reflecting a
>> >> different kind of conformational proximity (this is also discussed in
>> the
>> >> article). It's up to you to decide which one better suits your problem.
>> >>
>> >> Hope this helps.
>> >> Cheers,
>> >> Antonio
>> >>
>> >> Thank you very much for your reply Tsjerk.
>> > I understand that the two reference structures are different. I had a
>> query
>> > because I found the method is very sensitive to the choice of the
>> reference
>> > structure for fitting. Most of the publications either do not mention the
>> > reference structure. Only in few papers I found initial structure for
>> > fitting.

[gmx-users] Re: additional bond description (isopeptide bond) between two chains

2013-02-12 Thread durdagis

Justin, it's not the artifacts of visualization program. At the beginning
distance for isopeptide bond is 1.38 Angs (and it's defined at the
specbond.dat);

LYS NZ 1 GLY C 1 0.13LYQ GLQ

together with energy minimization this distance increases to around 3.0
Angs. (with normal termination).

However, when I continue to run for md sim. I am getting several LINCS
warnings (actually these relative constr. deviations are not at the
isopeptide bond).

Any suggestions how to handle this problem?

Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.031846, max 1.324710 (between atoms 4480 and 4482)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.3#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.3#
Wrote pdb files with previous and current coordinates

Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.038596, max 1.704050 (between atoms 4504 and 4506)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
4531 4546 57.30.2247 0.2305 0.1522
4531 4533 57.80.2243 0.2225 0.1526

--
View this message in context:
http://gromacs.5086.n6.nabble.com/additional-bond-description-isopeptide-bond-between-two-chains-tp5005445p5005455.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: additional bond description (isopeptide bond) between two chains

2013-02-12 Thread Justin Lemkul

On 2/12/13 8:37 AM, durdagis wrote:

Justin, it's not the artifacts of visualization program. At the beginning
distance for isopeptide bond is 1.38 Angs (and it's defined at the
specbond.dat);

LYS NZ 1 GLY C 1 0.13LYQ GLQ

together with energy minimization this distance increases to around 3.0
Angs. (with normal termination).

OK, this was not clear from the picture you showed. The text in the
representation is not very legible, so it seemed like the bond length was
normal. If, after energy minimization, the bond length is incorrect, you should
stop and investigate its source:

1. Is the bond present in the topology? Bonds can only occur within a single
[moleculetype] so multiple chains must be merged appropriately with pdb2gmx options.

2. Are you using constraints during EM?

However, when I continue to run for md sim. I am getting several LINCS
warnings (actually these relative constr. deviations are not at the
isopeptide bond).

Any suggestions how to handle this problem?

Go back and solve the EM issue before blindly plowing ahead.

-Justin

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.3#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.3#
Wrote pdb files with previous and current coordinates

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] velocity was not present from trjconv

2013-02-12 Thread Albert


Hello:

 I am using Gromacs4.6 and I extract one of my frame into .gro file by 
command:


trjconv_mpi -f md.xtc -s md.tpr -dump 25000 -o md.gro

I found that the velocity information was not present in this 
25ns-md.gro file:




Generated by trjconv : Protein t= 25000.0
54178
1TYR  N1   1.696   3.993   8.140
1TYR H12   1.658   4.068   8.196
1TYR H23   1.719   4.031   8.050
1TYR H34   1.630   3.919   8.122
1TYR CA5   1.822   3.938   8.210
1TYR HA6   1.865   4.020   8.268
1TYR CB7   1.790   3.814   8.300
1TYRHB18   1.883   3.770   8.336
1TYRHB29   1.764   3.732   8.233
1TYR CG   10   1.696   3.845   8.416
1TYRCD1   11   1.745   3.930   8.520
1TYRHD1   12   1.847   3.967   8.520
...

Does anybody knows what happen? The final md output md.gro file do 
contains velocity information:


Protein
54178
1TYR  N1   1.747   4.039   8.153 -0.1860  0.0829  0.0094
1TYR H12   1.694   4.084   8.226  2.0932 -0.4724  2.1614
1TYR H23   1.804   4.115   8.117 -1.6223  0.9380 -0.5483
1TYR H34   1.682   4.001   8.086  0.6678 -0.6031 -0.4474
1TYR CA5   1.826   3.927   8.204 -0.5364 -0.8546 -0.6273
1TYR HA6   1.892   3.958   8.285  0.3239 -2.3918 -0.7049
1TYR CB7   1.732   3.813   8.243  0.4625 -0.6033 -0.2530
1TYRHB18   1.791   3.725   8.265 -1.7147 -1.9740  0.4749
1TYRHB29   1.660   3.783   8.166 -0.2485  2.0549 -0.7384
1TYR CG   10   1.663   3.842   8.377 -0.0029  0.0693 -0.2885
1TYRCD1   11   1.739   3.893   8.481 -0.5325 -0.8010 -0.1664
1TYRHD1   12   1.841   3.925   8.465  0.0708 -2.2306  0.7255
1TYRCE1   13   1.680   3.925   8.606  0.5957  0.0504 -0.4752
1TYRHE1   14   1.728   3.974   8.689  1.1798 -3.6443  1.5406


THX

Albert
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] velocity was not present from trjconv

2013-02-12 Thread Justin Lemkul




On 2/12/13 9:17 AM, Albert wrote:

Hello:

  I am using Gromacs4.6 and I extract one of my frame into .gro file by command:

trjconv_mpi -f md.xtc -s md.tpr -dump 25000 -o md.gro

I found that the velocity information was not present in this 25ns-md.gro file:



Velocities are not stored in .xtc files.  They are stored in .trr files, if 
nstvout != 0 in the .mdp file.


-Justin




Generated by trjconv : Protein t= 25000.0
54178
 1TYR  N1   1.696   3.993   8.140
 1TYR H12   1.658   4.068   8.196
 1TYR H23   1.719   4.031   8.050
 1TYR H34   1.630   3.919   8.122
 1TYR CA5   1.822   3.938   8.210
 1TYR HA6   1.865   4.020   8.268
 1TYR CB7   1.790   3.814   8.300
 1TYRHB18   1.883   3.770   8.336
 1TYRHB29   1.764   3.732   8.233
 1TYR CG   10   1.696   3.845   8.416
 1TYRCD1   11   1.745   3.930   8.520
 1TYRHD1   12   1.847   3.967   8.520
...

Does anybody knows what happen? The final md output md.gro file do contains
velocity information:

Protein
54178
 1TYR  N1   1.747   4.039   8.153 -0.1860  0.0829  0.0094
 1TYR H12   1.694   4.084   8.226  2.0932 -0.4724  2.1614
 1TYR H23   1.804   4.115   8.117 -1.6223  0.9380 -0.5483
 1TYR H34   1.682   4.001   8.086  0.6678 -0.6031 -0.4474
 1TYR CA5   1.826   3.927   8.204 -0.5364 -0.8546 -0.6273
 1TYR HA6   1.892   3.958   8.285  0.3239 -2.3918 -0.7049
 1TYR CB7   1.732   3.813   8.243  0.4625 -0.6033 -0.2530
 1TYRHB18   1.791   3.725   8.265 -1.7147 -1.9740  0.4749
 1TYRHB29   1.660   3.783   8.166 -0.2485  2.0549 -0.7384
 1TYR CG   10   1.663   3.842   8.377 -0.0029  0.0693 -0.2885
 1TYRCD1   11   1.739   3.893   8.481 -0.5325 -0.8010 -0.1664
 1TYRHD1   12   1.841   3.925   8.465  0.0708 -2.2306  0.7255
 1TYRCE1   13   1.680   3.925   8.606  0.5957  0.0504 -0.4752
 1TYRHE1   14   1.728   3.974   8.689  1.1798 -3.6443  1.5406


THX

Albert


--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] velocity was not present from trjconv

2013-02-12 Thread Albert


On 02/12/2013 03:19 PM, Justin Lemkul wrote:
Velocities are not stored in .xtc files.  They are stored in .trr 
files, if nstvout != 0 in the .mdp file.


-Justin 


Hi Justin:

 thanks for kind comments.  I used the following settings and I didn't 
generate .trr file:


nstxout= 0; Write coordinates to output .trr file every 2 ps
nstvout= 0; Write velocities to output .trr file every 2 ps
nstfout= 0
nstxtcout = 2
nstenergy= 1; Write energies to output .edr file every 2 ps
nstlog= 1; Write output to .log file every 2 ps


probably that's the reason why it didn't have velocity informations 
My md is still running, I am just wondering, is there any way to extract 
the last snapshot into .gro file with velocity information?


thanks

best
Albert
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] velocity was not present from trjconv

2013-02-12 Thread Justin Lemkul




On 2/12/13 9:25 AM, Albert wrote:

On 02/12/2013 03:19 PM, Justin Lemkul wrote:

Velocities are not stored in .xtc files.  They are stored in .trr files, if
nstvout != 0 in the .mdp file.

-Justin


Hi Justin:

  thanks for kind comments.  I used the following settings and I didn't generate
.trr file:

nstxout= 0; Write coordinates to output .trr file every 2 ps
nstvout= 0; Write velocities to output .trr file every 2 ps
nstfout= 0
nstxtcout = 2
nstenergy= 1; Write energies to output .edr file every 2 ps
nstlog= 1; Write output to .log file every 2 ps


probably that's the reason why it didn't have velocity informations My md is
still running, I am just wondering, is there any way to extract the last
snapshot into .gro file with velocity information?



Extract it from the .cpt file that corresponds to that frame.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] velocity was not present from trjconv

2013-02-12 Thread Albert


On 02/12/2013 03:28 PM, Justin Lemkul wrote:

Extract it from the .cpt file that corresponds to that frame.

-Justin 


thanks a lot for such helpful comments. I found that the md production 
produced two .cpt file:


 state.cpt
state_prev.cpt

I am not sure which one would be the one I need Do you have any idea 
for this?


thanks again for kind helps.

best
Albert


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] velocity was not present from trjconv

2013-02-12 Thread Justin Lemkul




On 2/12/13 9:32 AM, Albert wrote:

On 02/12/2013 03:28 PM, Justin Lemkul wrote:

Extract it from the .cpt file that corresponds to that frame.

-Justin


thanks a lot for such helpful comments. I found that the md production produced
two .cpt file:

  state.cpt
state_prev.cpt

I am not sure which one would be the one I need Do you have any idea for 
this?



gmxcheck is your friend, as well as the wiki.

http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File

A checkpoint file is always written at the last step of the simulation, which 
seems to be what you were asking for previously.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] velocity was not present from trjconv

2013-02-12 Thread Albert


On 02/12/2013 03:33 PM, Justin Lemkul wrote:




gmxcheck is your friend, as well as the wiki.

http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File

A checkpoint file is always written at the last step of the 
simulation, which seems to be what you were asking for previously.


-Justin



IC. that's really helpful.

thanks a lot

Albert
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] can we schedule it?

2013-02-12 Thread Albert


Hello:

 I've got a question for setting of .mdp file for MD productions. The 
.trr file is really huge if we are going to run longer MD simulations. 
In this case, I usually only consider generate .xtc file, but the 
velocity is missed for all steps except the last one.


 So I am just wondering, can specify some parameters in the .mdp file 
so that Gromacs can export a .gro file with velocity information every 
20 ns?


thank you very much
best
Albert
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] can we schedule it?

2013-02-12 Thread Justin Lemkul




On 2/12/13 9:45 AM, Albert wrote:

Hello:

  I've got a question for setting of .mdp file for MD productions. The .trr file
is really huge if we are going to run longer MD simulations. In this case, I
usually only consider generate .xtc file, but the velocity is missed for all
steps except the last one.

  So I am just wondering, can specify some parameters in the .mdp file so that
Gromacs can export a .gro file with velocity information every 20 ns?



No, but if you only care about velocity information every 20 ns, then just set 
nstxout and nstvout = however many steps corresponds to 20 ns.  There is no need 
for the .trr to be huge if you don't need it to be.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] different springs - WHAM

2013-02-12 Thread Justin Lemkul




On 2/12/13 9:40 AM, Steven Neumann wrote:

Dear Gmx Users,

I know it is possible to combine windows with different spring
constants into the one PMF curve using g_wham.

Do I have to somehow tell g_wham that one or two windows have
different spring constants?



No, they are read from the .tpr files.


For instance - I got the better histogram overlap with lower force
constant in one window. When I replace this window into the window
with the sring constant like all windwos (worse overlap) both PMF
curves differ app. 2kcal/mol which is around 30% of the overall
deltaG.

Is there any error I should inroduce when one window differ in terms of k1?



What does g_wham's error analysis suggest?

-Justin


The deltaG value of my PMF with all the same windows (springs) is the
exact experimental value but has worse overlap.

Can you advise?

Steven



--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] different springs - WHAM

2013-02-12 Thread Steven Neumann

On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul  wrote:
>
>
> On 2/12/13 9:40 AM, Steven Neumann wrote:
>>
>> Dear Gmx Users,
>>
>> I know it is possible to combine windows with different spring
>> constants into the one PMF curve using g_wham.
>>
>> Do I have to somehow tell g_wham that one or two windows have
>> different spring constants?
>>
>
> No, they are read from the .tpr files.
>
>
>> For instance - I got the better histogram overlap with lower force
>> constant in one window. When I replace this window into the window
>> with the sring constant like all windwos (worse overlap) both PMF
>> curves differ app. 2kcal/mol which is around 30% of the overall
>> deltaG.
>>
>> Is there any error I should inroduce when one window differ in terms of
>> k1?
>>
>
> What does g_wham's error analysis suggest?
>
> -Justin

In both PMF error estimate with bayesian bootstraping is app. 0.2 kcal/mol

>
>
>> The deltaG value of my PMF with all the same windows (springs) is the
>> exact experimental value but has worse overlap.
>>
>> Can you advise?
>>
>> Steven
>>
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] error in md.log files

2013-02-12 Thread vidhya sankar

Dear Justin Thank you for your reply,


   I have set the Restraint  Along the Z Axis .  as follows

#ifdef POSRES_WATER
 ; Position restraint for each water oxygen
   [ position_restraints ]
      i  funct       fcx        fcy        fcz
      1    1         0           0      100
  #endif


Are you using the correct define statement in the .mdp file, and is your #ifdef 
in the correct location in the topology ?

As you have Asked  above in previous mail i have used the 

define        =  -DPOSRES  -DPOSRES_WATER    in my .mdp file  My question is 


1) Should i use  -DPOSRES_WATER  statement or Not  in .mdp file  ?


Also I have used the #ifdef  statement in the correct location in the topology  
as follows 

.  

; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcx    fcy    fcz
   1    1    0  0 10
#endif


; Include topology for ions
#include "gromos53a6_lipid.ff/ions.itp"



2) in  My md.log files  I have got following Lines At The end of Every 100 
steps  While it runs Smoothly Without Any Error . 

Large VCM(group NA): -0.01457, -0.01793, -0.03262, Temp-cm: 
 inf
Large VCM(group NA): -0.00894, -0.07417, -0.08968, Temp-cm: 
 inf
Large VCM(group NA):  0.00260, -0.05862, -0.10835, Temp-cm: 
 inf
Large VCM(group NA):  0.02240,  0.06127, -0.08617, Temp-cm: 
 inf
Large VCM(group NA):  0.11406,  0.11506, -0.07386, Temp-cm: 
 inf
Large VCM(group NA):  0.16859,  0.05669, -0.03958, Temp-cm: 
 inf
Large VCM(group NA):  0.07832, -0.04243, -0.02288, Temp-cm: 
 inf
Large VCM(group NA): -0.05293, -0.02293, -0.03210, Temp-cm: 
 inf
Large VCM(group NA):  0.01289,  0.09823, -0.02071, Temp-cm: 
 inf
Large VCM(group NA):  0.09863,  0.18033,  0.03704, Temp-cm: 
 inf
Large VCM(group NA):  0.01632,  0.22306,  0.04888, Temp-cm: 
 inf
Large VCM(group NA): -0.04317,  0.22376, -0.02476, Temp-cm: 
 inf
Large VCM(group NA):  0.08154,  0.19584, -0.06280, Temp-cm: 
 inf
Large VCM(group NA):  0.23298,  0.14145,  0.00921, Temp-cm: 
 inf
Large VCM(group NA):  0.22764,  0.09442,  0.07858, Temp-cm: 
 inf
Large VCM(group NA):  0.09441,  0.07206,  0.02138, Temp-cm: 
 inf
Large VCM(group NA):  0.00187,  0.04563, -0.03987, Temp-cm: 
 inf
Large VCM(group NA):  0.05896,  0.00550,  0.02418, Temp-cm: 
 inf
Large VCM(group NA):  0.2,  0.04126,  0.11459, Temp-cm: 
 inf
DD  step 5199  vol min/aver 0.821  load imb.: force  1.3%

How to Eliminate The Above error ?

Thanks In Advance
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: what do Coul-SR, LJ-SR, Coul-14 and LJ-14 mean in g_energy

2013-02-12 Thread escajarro

Hello all,

I am afraid that, after reading all the documentation I could find about
Coul-SR and LJ-SR, I still do not understand what these terms account for.

I am running a simulation of one single polymer chain in water. My values
for cut-off radious are rlist=rcoulomb=rvdw=1.5, I am using PME for
calculation of electrostatics, and simple cut-off potentials without tail
corrections. My simulation box is large enough, so that the polymer chain
can not 'feel' its periodic images. Nevertheless, the terms
Coul-SR:Polymer-Polymer and LJ-SR:Polymer-Polymer are not zero, as I would
expect if they were the (short-range) interaction of one polymer chain with
a different one. It is also not the short-range interaction of the polymer
with itself, as they are also different from the terms
Coul-14:Polymer-Polymer and LJ-14:Polymer-Polymer energies. Are then the SR
terms equal to the 14 terms plus the exclusion terms? If not, what energy
contributions contain the SR terms?

Thanks

--
View this message in context:
http://gromacs.5086.n6.nabble.com/what-do-Coul-SR-LJ-SR-Coul-14-and-LJ-14-mean-in-g-energy-tp4450921p5005471.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Intra-protein hydrophobic contacts

2013-02-12 Thread Justin Lemkul




On 2/12/13 11:29 AM, Kavyashree M wrote:

Dear Users,

How can intra-protein hydrophobic contacts be found
for a trajectory. Most of the mails regarding this in the
list is regarding hydrophobic contacts between chains
or ligand and protein. So kindly help.



Create a group of hydrophobic atoms and choose that group at both prompts with 
g_mindist -on.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: what do Coul-SR, LJ-SR, Coul-14 and LJ-14 mean in g_energy

2013-02-12 Thread Justin Lemkul




On 2/12/13 11:06 AM, escajarro wrote:

Hello all,

I am afraid that, after reading all the documentation I could find about
Coul-SR and LJ-SR, I still do not understand what these terms account for.

I am running a simulation of one single polymer chain in water. My values
for cut-off radious are rlist=rcoulomb=rvdw=1.5, I am using PME for
calculation of electrostatics, and simple cut-off potentials without tail
corrections. My simulation box is large enough, so that the polymer chain
can not 'feel' its periodic images. Nevertheless, the terms
Coul-SR:Polymer-Polymer and LJ-SR:Polymer-Polymer are not zero, as I would
expect if they were the (short-range) interaction of one polymer chain with
a different one. It is also not the short-range interaction of the polymer
with itself, as they are also different from the terms
Coul-14:Polymer-Polymer and LJ-14:Polymer-Polymer energies. Are then the SR
terms equal to the 14 terms plus the exclusion terms? If not, what energy
contributions contain the SR terms?



Actually, the SR terms are indeed interactions of the polymer with itself.  1-4 
interactions are special interactions that occur between atoms separated by 3 
bonds.  SR stands for "short range," which encompasses all interactions that are 
not excluded by that occur within the shortest nonbonded cutoff.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] different springs - WHAM

2013-02-12 Thread Justin Lemkul




On 2/12/13 9:57 AM, Steven Neumann wrote:

On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul  wrote:



On 2/12/13 9:40 AM, Steven Neumann wrote:


Dear Gmx Users,

I know it is possible to combine windows with different spring
constants into the one PMF curve using g_wham.

Do I have to somehow tell g_wham that one or two windows have
different spring constants?



No, they are read from the .tpr files.



For instance - I got the better histogram overlap with lower force
constant in one window. When I replace this window into the window
with the sring constant like all windwos (worse overlap) both PMF
curves differ app. 2kcal/mol which is around 30% of the overall
deltaG.

Is there any error I should inroduce when one window differ in terms of
k1?



What does g_wham's error analysis suggest?

-Justin


In both PMF error estimate with bayesian bootstraping is app. 0.2 kcal/mol



Seems like a good result, so what's the problem?

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] error in md.log files

2013-02-12 Thread Justin Lemkul




On 2/12/13 10:29 AM, vidhya sankar wrote:

Dear Justin Thank you for your reply,


I have set the Restraint  Along the Z Axis .  as follows

#ifdef POSRES_WATER
  ; Position restraint for each water oxygen
[ position_restraints ]
   i  funct   fcxfcyfcz
   11 0   0  100
   #endif


Are you using the correct define statement in the .mdp file, and is your #ifdef 
in the correct location in the topology ?

As you have Asked  above in previous mail i have used the

define=  -DPOSRES  -DPOSRES_WATERin my .mdp file  My question is


1) Should i use  -DPOSRES_WATER  statement or Not  in .mdp file  ?



If you want the restraint, then yes.  This seems correct.



Also I have used the #ifdef  statement in the correct location in the topology  
as follows

.

; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
110  0 10
#endif


; Include topology for ions
#include "gromos53a6_lipid.ff/ions.itp"



2) in  My md.log files  I have got following Lines At The end of Every 100 
steps  While it runs Smoothly Without Any Error .

Large VCM(group NA): -0.01457, -0.01793, -0.03262, Temp-cm: 
 inf
Large VCM(group NA): -0.00894, -0.07417, -0.08968, Temp-cm: 
 inf
Large VCM(group NA):  0.00260, -0.05862, -0.10835, Temp-cm: 
 inf
Large VCM(group NA):  0.02240,  0.06127, -0.08617, Temp-cm: 
 inf
Large VCM(group NA):  0.11406,  0.11506, -0.07386, Temp-cm: 
 inf
Large VCM(group NA):  0.16859,  0.05669, -0.03958, Temp-cm: 
 inf
Large VCM(group NA):  0.07832, -0.04243, -0.02288, Temp-cm: 
 inf
Large VCM(group NA): -0.05293, -0.02293, -0.03210, Temp-cm: 
 inf
Large VCM(group NA):  0.01289,  0.09823, -0.02071, Temp-cm: 
 inf
Large VCM(group NA):  0.09863,  0.18033,  0.03704, Temp-cm: 
 inf
Large VCM(group NA):  0.01632,  0.22306,  0.04888, Temp-cm: 
 inf
Large VCM(group NA): -0.04317,  0.22376, -0.02476, Temp-cm: 
 inf
Large VCM(group NA):  0.08154,  0.19584, -0.06280, Temp-cm: 
 inf
Large VCM(group NA):  0.23298,  0.14145,  0.00921, Temp-cm: 
 inf
Large VCM(group NA):  0.22764,  0.09442,  0.07858, Temp-cm: 
 inf
Large VCM(group NA):  0.09441,  0.07206,  0.02138, Temp-cm: 
 inf
Large VCM(group NA):  0.00187,  0.04563, -0.03987, Temp-cm: 
 inf
Large VCM(group NA):  0.05896,  0.00550,  0.02418, Temp-cm: 
 inf
Large VCM(group NA):  0.2,  0.04126,  0.11459, Temp-cm: 
 inf
DD  step 5199  vol min/aver 0.821  load imb.: force  1.3%

How to Eliminate The Above error ?



"Group NA" seems to imply that you are coupling solvent and ions to separate 
thermostats, which is a terrible idea.  The ions are moving separately from 
water and they are crashing into one another.  You may have to restrain the ions 
in some way if you are also restraining water to prevent such collisions.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Error: The Y-size of the box times the triclinic skew factor is smaller than the number of DD cells times the smallest allowed cell size

2013-02-12 Thread Sonia Aguilera

Hi, 

I was performing a NPT calculation, and I got this error:

The Y-size of the box (6.002812) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (6) times the smallest allowed cell
size (1.000605)

I also tried to change the number of processors but I got the same error. My
system is a protein in vacuo. This is my mdp file (Taken from Justin
Lemkul's tutorial for FE calculations:

title= NPT equilibration
; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.002
nsteps   = 20; 00 ps
nstcomm  = 100
;Langevin dynamics
ld_seed  = -1
; Output control
nstxout  = 1000
nstvout  = 1000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxtcout= 0
xtc-precision= 1000
; Neighborsearching and short-range nonbonded interactions
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.5
; Electrostatics
coulombtype  = PME
rcoulomb = 1.5
; van der Waals
vdw-type = switch
rvdw-switch  = 0.8
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
optimize_fft = no
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = system
tau_t= 1.0
ref_t= 300
; Pressure coupling is on for NPT
Pcoupl   = Parrinello-Rahman
tau_p= 0.5
compressibility  = 4.5e-05
ref_p= 1.0
; Do not generate velocities
gen_vel  = no
; options for bonds
constraints  = h-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Constrain the starting configuration
; since we are continuing from NVT
continuation = yes
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 12


Can you please tell my what is wrong? I runned previous nvt, npt and md
simulation with the same box size and protein but in water. Is there any way
of solving this problem without affecting the accuracy of the simulation?

Thank you in advance

Sonia Aguilera





--
View this message in context: 
http://gromacs.5086.n6.nabble.com/Error-The-Y-size-of-the-box-times-the-triclinic-skew-factor-is-smaller-than-the-number-of-DD-cells-te-tp5005483.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Error: The Y-size of the box times the triclinic skew factor is smaller than the number of DD cells times the smallest allowed cell size

2013-02-12 Thread Justin Lemkul




On 2/12/13 5:24 PM, Sonia Aguilera wrote:

Hi,

I was performing a NPT calculation, and I got this error:

The Y-size of the box (6.002812) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (6) times the smallest allowed cell
size (1.000605)

I also tried to change the number of processors but I got the same error. My
system is a protein in vacuo. This is my mdp file (Taken from Justin
Lemkul's tutorial for FE calculations:

title= NPT equilibration
; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.002
nsteps   = 20; 00 ps
nstcomm  = 100
;Langevin dynamics
ld_seed  = -1
; Output control
nstxout  = 1000
nstvout  = 1000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxtcout= 0
xtc-precision= 1000
; Neighborsearching and short-range nonbonded interactions
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.5
; Electrostatics
coulombtype  = PME
rcoulomb = 1.5
; van der Waals
vdw-type = switch
rvdw-switch  = 0.8
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
optimize_fft = no
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = system
tau_t= 1.0
ref_t= 300
; Pressure coupling is on for NPT
Pcoupl   = Parrinello-Rahman
tau_p= 0.5
compressibility  = 4.5e-05
ref_p= 1.0
; Do not generate velocities
gen_vel  = no
; options for bonds
constraints  = h-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Constrain the starting configuration
; since we are continuing from NVT
continuation = yes
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 12


Can you please tell my what is wrong? I runned previous nvt, npt and md
simulation with the same box size and protein but in water. Is there any way
of solving this problem without affecting the accuracy of the simulation?



NPT doesn't make sense in vacuo.  The unit cell compresses around the protein, 
leaving you with periodicity artifacts and a quasi-crystalline environment.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: Error: The Y-size of the box times the triclinic skew factor is smaller than the number of DD cells times the smallest allowed cell size

2013-02-12 Thread Sonia Aguilera

Thank you Justin, 

So, your advice is not to perform the npt calculation and to run the md
after the nvt?

Thank you, 

Sonia Aguilera



--
View this message in context: 
http://gromacs.5086.n6.nabble.com/Error-The-Y-size-of-the-box-times-the-triclinic-skew-factor-is-smaller-than-the-number-of-DD-cells-te-tp5005483p5005485.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: Error: The Y-size of the box times the triclinic skew factor is smaller than the number of DD cells times the smallest allowed cell size

2013-02-12 Thread Justin Lemkul




On 2/12/13 5:44 PM, Sonia Aguilera wrote:

Thank you Justin,

So, your advice is not to perform the npt calculation and to run the md
after the nvt?



A common mistake is to think that there is a "standard" protocol that one must 
follow.  While it is true that for the condensed phase, a common procedure 
involves restrained NVT and NPT prior to production simulations under an NPT 
ensemble, this protocol is by no means necessary or appropriate under all 
conditions.  Simulating in vacuo requires different procedures and .mdp 
settings.  This topic has been discussed several times just in the last week or 
two; please refer to the list archive for useful information.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] installation

2013-02-12 Thread David Sáez

Hello everybody, I'm trying to install Gromacs 4.6 in my Ubuntu 12.04
laptop. As I am not a a skilled user, I tried the Quick and Dirty
Installation, After following the instructions I obtained this message when
trying to execute GMXRC:

david@HAL-9000:~$ /usr/local/gromacs/bin/GMXRC
/usr/local/gromacs/bin/GMXRC: line 34: return: can only `return' from a
function or sourced script
/usr/local/gromacs/bin/GMXRC: line 43: CSH:: command not found
/usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected
token `setenv'
/usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv
LD_LIBRARY_PATH ""'

Could someone give some help?

Thanks in advance.



-- 
David A. Sáez San Martín
Químico-Farmacéutico
Concepción, Chile
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] installation

2013-02-12 Thread Justin Lemkul




On 2/12/13 9:24 PM, David Sáez wrote:

Hello everybody, I'm trying to install Gromacs 4.6 in my Ubuntu 12.04
laptop. As I am not a a skilled user, I tried the Quick and Dirty
Installation, After following the instructions I obtained this message when
trying to execute GMXRC:

david@HAL-9000:~$ /usr/local/gromacs/bin/GMXRC
/usr/local/gromacs/bin/GMXRC: line 34: return: can only `return' from a
function or sourced script
/usr/local/gromacs/bin/GMXRC: line 43: CSH:: command not found
/usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected
token `setenv'
/usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv
LD_LIBRARY_PATH ""'

Could someone give some help?



Note the first error - you need to source the file.

$ source /usr/local/gromacs/bin/GMXRC

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Need advice on appending aa residues to the sequence

2013-02-12 Thread zugunder

Hi,

I am sorry if this topic is not relevant for GROMACS forum, but I hope
someone has faced the same problem before and could give me some advice...

I need to simulate a relatively short protein (170aa) in water. No
structures are available for it, so I used a Modeller web server to get
some. Unfortunately, they only provided me with several truncated structures
(with relatively high scores though) of 40 and 130aa length. However, they
do not overlap and the gap is 4aa long. While doing a research on the better
way to stitch them I ran a couple of simulations of 2 most high scoring
structures for a 130fragment (C-term) and one of them seems to fold
relatively quickly.
The problem now is that I can't find a way to append those 4 residues to
either of the sequences and stitch them into one to simulate the complete
thing. I found several references to DeepView software, but it does not seem
to work in my hands (or probably I am missing something).
So if someone has faced the same problem or has any ideas on how to do this
kind of reconstruction of the sequence for further simulation, I'd really
appreciate any tips, advice or other input.

Thank you.

--
View this message in context:
http://gromacs.5086.n6.nabble.com/Need-advice-on-appending-aa-residues-to-the-sequence-tp5005489.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] installation

2013-02-12 Thread David Sáez

Thanks for your answer Justin. I followed your advice:
When I type
*$ source /usr/local/gromacs/bin/GMXRC*
*$*

Nothing happened, the prompt returns normally and no action is executed. Do
you have any idea?


On Tue, Feb 12, 2013 at 11:27 PM, Justin Lemkul  wrote:

>
>
> On 2/12/13 9:24 PM, David Sáez wrote:
>
>> Hello everybody, I'm trying to install Gromacs 4.6 in my Ubuntu 12.04
>> laptop. As I am not a a skilled user, I tried the Quick and Dirty
>> Installation, After following the instructions I obtained this message
>> when
>> trying to execute GMXRC:
>>
>> david@HAL-9000:~$ /usr/local/gromacs/bin/GMXRC
>> /usr/local/gromacs/bin/GMXRC: line 34: return: can only `return' from a
>> function or sourced script
>> /usr/local/gromacs/bin/GMXRC: line 43: CSH:: command not found
>> /usr/local/gromacs/bin/GMXRC.**csh: line 8: syntax error near unexpected
>> token `setenv'
>> /usr/local/gromacs/bin/GMXRC.**csh: line 8: `if (! $?LD_LIBRARY_PATH)
>> setenv
>> LD_LIBRARY_PATH ""'
>>
>> Could someone give some help?
>>
>>
> Note the first error - you need to source the file.
>
> $ source /usr/local/gromacs/bin/GMXRC
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
David A. Sáez San Martín
Químico-Farmacéutico
Concepción, Chile
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] number denisty calculation

2013-02-12 Thread Rajalakshmi.C

hi all,
i am trying to find the coordination number using the rdf between two chains
in the system .my box contains two polymer chains with water molecules.i know
integrating 4*pi*r*r*g(r)*rho between 0 to first minima of rdf will give
coordination number .the first minima value i took from the rdf between two
chains. but for value of rho what shall i use .is that total number of
atoms/volume of box or number of atoms in the two chains/volume of box. i have
a doubt whether to include number of solvent atoms to calculate the number
density or not .kindly clarify this doubt
--
Open WebMail Project (http://openwebmail.org)

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: gmx-users Digest, Vol 106, Issue 62

2013-02-12 Thread neeru sharma

>
> On 2/12/13 1:12 AM, neeru sharma wrote:
> > Dear Gromacs Users,
> >
> >
> > I have simulated a system of protein-ion complex. As a part of the
> > analysis, I want to see whether there are any H-bonds or other
> interactions
> > between the active site residues and the water surrounding those
> residues.
> > I was trying to perform the same using g_hbond program of gromacs, but
> > could not get any output. I tried with varying the cut off value and as
> > well specifying the "contact" option to look for the non H-bond
> > interactions too, that fall within the cut off mentioned.
> >
> > Can anybody suggest me how to look for the H-bonds between protein
> residues
> > and water molecules?
> >
>
> Your question and subject line refer to different things.  Detecting
> hydrogen
> bonds between protein residues and water is trivial.  Create index groups
> for
> the residues of interest and select these residues and water as the two
> groups
> for g_hbond.  Water-mediated hydrogen bonds between residues, however, are
> far
> more difficult to obtain, but this topic has been covered many times in
> the list
> archive.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
>
> -
>
Thanks Justin.
It worked. Earlier I was trying just with the index file of the specific
residues and without the index file for the specific water molecules. But
now it works when I give the  index file both for specific water and
protein residues.


--Neeru
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

39 matches

Mail list logo