[gmx-users] Re: Looking for GPU benchmarks

[Mathieu38]

OK. Which version / branch / revision should I use then ?

Thanks.



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Re: [gmx-users] Re: Cross-correlation maps

[Tsjerk Wassenaar]

Hey,

In addition to Newton's cradle, there's also Columbus' egg. To make it
stand, you smash it slightly, pressing one end. If you do PCA on that,
you'll find a collective motion involving both the smashed end as well
as the opposite, unscathed end. That accounts for the greater part of
the global, end-to-end collective motions you see when you analyze the
backbone. You don't have that when looking at the more subtle side
chain motions.

Cheers,

Tsjerk


On Tue, Aug 28, 2012 at 8:34 AM, Mark Abraham  wrote:
> On 28/08/2012 4:09 PM, James Starlight wrote:
>>
>> Mark,
>>
>> Thanks for explanation!
>>
>>
>> 2012/8/27, Mark Abraham :
>>
>>> Did you construct a correlation matrix from side chain atoms?
>>
>> Yes, and there is some degree of correlation between adjacent side
>> chains but lack of any cooperativety between distant side-chains. In
>> comparison in that protein there were alot of cooperativity in motion
>> of the distinct backbones.
>
>
> Then that might be the conclusion, but that's your judgement to make from
> the full context. It's hardly likely that there'd be magical "action at a
> distance," but motion along the lines of Newton's cradle could have been
> detected and would be fascinating to see in a protein (e.g.
> http://www.youtube.com/watch?v=H7P4xOUPYVw). Motion exactly like Newton's
> cradle does require cross-correlation to observe, because of the intrinsic
> asynchronicity, but that would require particular plasticity conditions.
>
>
>>   I suppose that it might be due to the
>> relatively limited degree of freedom of the backbones (2 dihedrals
>> with 3 minimum conformations) in comparison to the side-chains so the
>> correlation in the backbone might be more expected.
>
>
> Backbone atoms can only move in concert with others, yes.
>
>
>>
>> In addition as I've told you during analysis of filtered.xtc processed
>> trajectory I didnt observe any fluctuations of side chains on the
>> whole.
>
>
> Yes, but the amplitude of single-side-chain motions is necessarily small, so
> it doesn't follow that you should observe it in the eigenvectors with the
> largest fluctuations. There's no direct connection to the energy required
> for such motions, either. You should be looking at some small peptide
> systems to learn how to make observations of motion you know occurs, before
> trying to observe hypothesized motion.
>
>
>>Finally I've noticed some bugs in the visualistion of the
>> side-chains of the structures processed after g_covar  ( e.g
>> EDA_average.pdb) In that case the geometry of some side-chains (mainly
>> of aromatic rings)  were very distorted. Why this might occur ?
>
>
> http://www.gromacs.org/Documentation/Terminology/Average_Structure
>
> Mark
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Re: Cross-correlation maps

[Mark Abraham]

On 28/08/2012 4:09 PM, James Starlight wrote:

Mark,

Thanks for explanation!


2012/8/27, Mark Abraham :


Did you construct a correlation matrix from side chain atoms?

Yes, and there is some degree of correlation between adjacent side
chains but lack of any cooperativety between distant side-chains. In
comparison in that protein there were alot of cooperativity in motion
of the distinct backbones.


Then that might be the conclusion, but that's your judgement to make 
from the full context. It's hardly likely that there'd be magical 
"action at a distance," but motion along the lines of Newton's cradle 
could have been detected and would be fascinating to see in a protein 
(e.g. http://www.youtube.com/watch?v=H7P4xOUPYVw). Motion exactly like 
Newton's cradle does require cross-correlation to observe, because of 
the intrinsic asynchronicity, but that would require particular 
plasticity conditions.



  I suppose that it might be due to the
relatively limited degree of freedom of the backbones (2 dihedrals
with 3 minimum conformations) in comparison to the side-chains so the
correlation in the backbone might be more expected.


Backbone atoms can only move in concert with others, yes.



In addition as I've told you during analysis of filtered.xtc processed
trajectory I didnt observe any fluctuations of side chains on the
whole.


Yes, but the amplitude of single-side-chain motions is necessarily 
small, so it doesn't follow that you should observe it in the 
eigenvectors with the largest fluctuations. There's no direct connection 
to the energy required for such motions, either. You should be looking 
at some small peptide systems to learn how to make observations of 
motion you know occurs, before trying to observe hypothesized motion.



   Finally I've noticed some bugs in the visualistion of the
side-chains of the structures processed after g_covar  ( e.g
EDA_average.pdb) In that case the geometry of some side-chains (mainly
of aromatic rings)  were very distorted. Why this might occur ?


http://www.gromacs.org/Documentation/Terminology/Average_Structure

Mark
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Re: [gmx-users] Re: Cross-correlation maps

[James Starlight]

Mark,

Thanks for explanation!


2012/8/27, Mark Abraham :

> Did you construct a correlation matrix from side chain atoms?

Yes, and there is some degree of correlation between adjacent side
chains but lack of any cooperativety between distant side-chains. In
comparison in that protein there were alot of cooperativity in motion
of the distinct backbones. I suppose that it might be due to the
relatively limited degree of freedom of the backbones (2 dihedrals
with 3 minimum conformations) in comparison to the side-chains so the
correlation in the backbone might be more expected.

In addition as I've told you during analysis of filtered.xtc processed
trajectory I didnt observe any fluctuations of side chains on the
whole.  Finally I've noticed some bugs in the visualistion of the
side-chains of the structures processed after g_covar  ( e.g
EDA_average.pdb) In that case the geometry of some side-chains (mainly
of aromatic rings)  were very distorted. Why this might occur ?
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Re: [gmx-users] Re: Cross-correlation maps

[Mark Abraham]

On 28/08/2012 3:09 PM, James Starlight wrote:

Hi Tsjerk!

Normally during analysis of the MD trajectory I've observed frequent
side-chain fluctuations (ps timescale) cased by the temperature motion
of the atoms as well as larger-scale backbone motions ( on the ns
time).

The ps  side-chains motions are known to especially increase total
enthropy of the system in comparison to the backbone dynamics where
such factor is less meaningful. Also there is suggestion that such
enthropy-dominated motions could be functional-relevant due to
possible coperativity of that process ( e.g fluctuations in one side
of protein case increase dynamics in another part of such molecule
without visible pathways between both parts )


So you're looking for correlated motion of atoms distant in space. That 
will appear as off-diagonal entries in the correlation matrix. Think 
about what sort of correlation matrices and eigenstructure you would 
expect for a system of a small number of SHM oscillators under different 
sorts of correlation conditions. Then worry about proteins.



The main goal of my study to find out such coperativity in some
proteins. So I want to detect such coperativity in fluctuations of the
side-chains. As I've found the only way to do it is the calculation of
the cross-correlation maps.


Cross-correlation is an analysis distinct from looking at off-diagonal 
(a.k.a. "cross") elements of a correlation matrix.



  When I've performed PCA of my 100ns
trajectory and examined filtered.xtc trajectory consisted of first 50
principal components) I didt observed any fluctuations of the
side-chains ( only backbone motions were presented) So I could
calculate only correlations in the backbone atoms motions. Is there
any way to observe such cross-correlations for side chains as well ?


Did you construct a correlation matrix from side chain atoms?

Mark



James

2012/8/27, Tsjerk Wassenaar :

Hi James,

Correlation is covariance normalized to variance. So you'll need the
covariance matrix anyway. But what exactly due you mean with the loss of
information, which you could solve with correlations?

Cheers,

Tsjerk

On Aug 27, 2012 4:01 PM, "James Starlight"  wrote:

Mark,

Is there any way to calculate such cross-correlations without
calculation of the covariance matrix ( from the MD trajectory
indirectly) ?
I've noticed that after processind of my trajectory with PCA method
some dynamics ( e.g fluctuations of the side-chains) are lost even
when I've analysed filtered.xtc from the first 50 principal
components. How I should analyse possible cross-correlations of the
fluctuations of the side-chains?

James

2012/8/27 Mark Abraham :


On 24/08/2012 4:51 PM, James Starlight wrote: >> >> up :) >> It's

appeared two additional question...
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Re: [gmx-users] Re: Cross-correlation maps

[James Starlight]

Hi Tsjerk!

Normally during analysis of the MD trajectory I've observed frequent
side-chain fluctuations (ps timescale) cased by the temperature motion
of the atoms as well as larger-scale backbone motions ( on the ns
time).

The ps  side-chains motions are known to especially increase total
enthropy of the system in comparison to the backbone dynamics where
such factor is less meaningful. Also there is suggestion that such
enthropy-dominated motions could be functional-relevant due to
possible coperativity of that process ( e.g fluctuations in one side
of protein case increase dynamics in another part of such molecule
without visible pathways between both parts )

The main goal of my study to find out such coperativity in some
proteins. So I want to detect such coperativity in fluctuations of the
side-chains. As I've found the only way to do it is the calculation of
the cross-correlation maps. When I've performed PCA of my 100ns
trajectory and examined filtered.xtc trajectory consisted of first 50
principal components) I didt observed any fluctuations of the
side-chains ( only backbone motions were presented) So I could
calculate only correlations in the backbone atoms motions. Is there
any way to observe such cross-correlations for side chains as well ?

James

2012/8/27, Tsjerk Wassenaar :
> Hi James,
>
> Correlation is covariance normalized to variance. So you'll need the
> covariance matrix anyway. But what exactly due you mean with the loss of
> information, which you could solve with correlations?
>
> Cheers,
>
> Tsjerk
>
> On Aug 27, 2012 4:01 PM, "James Starlight"  wrote:
>
> Mark,
>
> Is there any way to calculate such cross-correlations without
> calculation of the covariance matrix ( from the MD trajectory
> indirectly) ?
> I've noticed that after processind of my trajectory with PCA method
> some dynamics ( e.g fluctuations of the side-chains) are lost even
> when I've analysed filtered.xtc from the first 50 principal
> components. How I should analyse possible cross-correlations of the
> fluctuations of the side-chains?
>
> James
>
> 2012/8/27 Mark Abraham :
>
>> On 24/08/2012 4:51 PM, James Starlight wrote: >> >> up :) >> It's
> appeared two additional question...
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[gmx-users] mdrun_gpu on NVidia Quadro 2000

[Mauricio Carrillo Tripp]

Hi,

I was wondering if the numbers I get are reasonable while running the DHFR
benchmark at:
http://www.gromacs.org/Documentation/Installation_Instructions/GPUs

As you can see, CPU performance is quite good, but GPU performance is
really bad
compared with results on that page for other cards (Tesla, GTX):

Performance [ns/day]:
*benchCPU GPU*
dhfr-impl-1nm79.950  45.385
dhfr-impl-2nm25.072  44.961
dhfr-impl-inf17.597  25.737
dhfr-solv-PME24.168   4.454
dhfr-solv-RF-1nm 33.339   8.594
dhfr-solv-RF-2nm 6.1823.008

*Specs*
CPU: 2x Intel(R) Xeon(R) CPU X5675 @ 3.07GHz (24 Threads)
GPU: Matrox Graphics, Inc. MGA G200eW WPCM450 (rev 0a) NVIDIA Corporation
GF106GL [Quadro 2000] (rev a1) -- (
http://www.nvidia.com/object/product-quadro-2000-us.html)
Cuda compilation tools, release 4.2.9, V0.2.1221
(cudatoolkit_4.2.9_linux_64, gpucomputingsdk_4.2.9)
OpenMM 4.1.1-Linux64 (Is this a problem? Page says: the current Gromacs-GPU
release is compatible with OpenMM version 2.0)
Gromacs 4.5.5 (Compiled from source following directions at the above page)
Ubuntu 12.04

I do have to use the option: mdrun_gpu -device "OpenMM: force-device=yes" in
order for Gromacs to run.

If I'm doing things right, then I guess the bad performance is due to my
"incompatible" card. My question is if this will change/improve with
Gromacs 4.6?

Thanks!

--
Mauricio Carrillo Tripp

Biofísica Computacional - Bioinformática

LAboratorio Nacional de GEnómica para la BIOdiversidad

Centro de INVestigación y ESTudios AVanzados
Km 9.6 Libramiento Norte Carretera a León
36821 Irapuato, Gto., México
Tel. oficina: (+52) 462 166-3019
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Re: [gmx-users] Problem with incorrect GB-Polarization Energy Value

[Mark Abraham]

On 28/08/2012 2:33 AM, jesmin jahan wrote:

Dear All,

I am using Gromacs 4.5.3 for GB-Polarization Energy Calculation. As I
am not interested to any other energy terms right now, I have set all
the non-bonded parameters to 0.

I am also calculating GB polarization energy using other available
Molecular Dynamic Packages and doing a comparative study between them
(say: Accuracy Vs. Speed Up).
I have already used Gromacs for calculating GB-energy for 168
different Protein molecules and the energy values reported were more
or less the same as reported by others.

Now, I am using a virus shell as input in this process. It contains
1.5 million atoms. Unfortunately, this time, the energy reported is
almost half of the value reported by others.
So, I am a little bit confused. Am I doing something wrong? I have
heard previously that there is no max size for Gromacs.


Probably you're comparing apples with oranges. Your previous reports 
were choosing to use a cut-off in the non-bonded interactions. Perhaps 
some of the other codes are not or cannot. That would greatly affect 
performance and the value of the result, and is part of why it is 
meaningless to try to extract the time for just a part of a calculation 
without the timing of its support infrastructure (such as constructing 
the pair list from the cut-off). Also, since you are computing on 
proteins, you probably have bonded and VDW interactions in your force 
field also, and your timing comparisons will be misleading if you ignore 
those. The time taken to execute an implementation of a complex 
algorithm is rarely additive in its parts. For example, software that 
makes good or bad use of the cache in a real calculation won't have the 
opportunity to show that if the whole problem size fits in the L1 cache 
because it's been stripped down.


Mark
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Re: [gmx-users] Question about Multi-level parallelization: MPI and OpenMP

[jesmin jahan]

Okay Mark, Thanks!.

Best Regards,
Jesmin

On Mon, Aug 27, 2012 at 6:15 PM, Mark Abraham  wrote:
> On 28/08/2012 2:40 AM, jesmin jahan wrote:
>>
>> Dear Gromacs Users,
>>
>> I have two questions about the multi-level parallelism of Gromacs.
>>
>> http://www.gromacs.org/Documentation/Acceleration_and_parallelization?highlight=verlet#GPU_acceleration
>>
>> 1. Is this feature is only supported by Gromacs 4.6? Or we can get it
>> in 4.5.3 also?
>
>
> That section of that page is pretty specific about versions. The shiny new
> stuff is due in 4.6.
>
>
>> 2. In Gromacs 4.5.3, I have used OMP_NUM_THREADS=12 mpirun -np 16
>> mdrun_mpi -s imd.tpr command to run 16 gromacs processes each with 12
>> threads.
>>
>> In the log file, I can see
>>
>>   nodeid: 0  nnodes:  16
>>
>> Its clear that 16 nodes are being used in work load distribution. But
>> its not clear whether 12 thread is being used in each of those
>> processes /nodes because there is no mention about the number of
>> threads.
>>
>> Does anyone know about this?
>
>
> Again from that page: "With GROMACS 4.6 OpenMP multithreading is
> supported..."
>
> Mark
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-- 
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
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Re: [gmx-users] Question about Multi-level parallelization: MPI and OpenMP

[Mark Abraham]

On 28/08/2012 2:40 AM, jesmin jahan wrote:

Dear Gromacs Users,

I have two questions about the multi-level parallelism of Gromacs.
http://www.gromacs.org/Documentation/Acceleration_and_parallelization?highlight=verlet#GPU_acceleration

1. Is this feature is only supported by Gromacs 4.6? Or we can get it
in 4.5.3 also?


That section of that page is pretty specific about versions. The shiny 
new stuff is due in 4.6.



2. In Gromacs 4.5.3, I have used OMP_NUM_THREADS=12 mpirun -np 16
mdrun_mpi -s imd.tpr command to run 16 gromacs processes each with 12
threads.

In the log file, I can see

  nodeid: 0  nnodes:  16

Its clear that 16 nodes are being used in work load distribution. But
its not clear whether 12 thread is being used in each of those
processes /nodes because there is no mention about the number of
threads.

Does anyone know about this?


Again from that page: "With GROMACS 4.6 OpenMP multithreading is 
supported..."


Mark
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Re: [gmx-users] Incorrect bond in top file

[Justin Lemkul]

On 8/27/12 3:03 PM, Shima Arasteh wrote:



OK, I checked the bonds section of top, there  is no bond between CN and HN.

Thanks for it.

But there is a new problem.

I passed the steps for simulation the protein in water, up to the EM step. I 
ran grompp and then mdrun to do energy minimization. I see the protein broken. 
As you said in another email asked a few hours ago, I ran the command trjconv :
# trjconv -s EM.tpr -f EM.gro -pbc mol -ur compact -o EM_pbc.gro

I still see the protein broken.The FVAL is not connected to the next residue. 
Would you let me know your idea? Is there any trick here?



Your .rtp entry needs a bond between the C of FVAL and the N of the next 
residue, i.e.:


C +N

in the [bonds] directive.

Again, in general, be advised that nothing you see in visualization software is 
definitive; only the topology is.  In this case, going back to your .rtp entry, 
I suspect that the bond is, in fact, absent.


-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


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Re: [gmx-users] Re: Cross-correlation maps

[Tsjerk Wassenaar]

Hi James,

Correlation is covariance normalized to variance. So you'll need the
covariance matrix anyway. But what exactly due you mean with the loss of
information, which you could solve with correlations?

Cheers,

Tsjerk

On Aug 27, 2012 4:01 PM, "James Starlight"  wrote:

Mark,

Is there any way to calculate such cross-correlations without
calculation of the covariance matrix ( from the MD trajectory
indirectly) ?
I've noticed that after processind of my trajectory with PCA method
some dynamics ( e.g fluctuations of the side-chains) are lost even
when I've analysed filtered.xtc from the first 50 principal
components. How I should analyse possible cross-correlations of the
fluctuations of the side-chains?

James

2012/8/27 Mark Abraham :

> On 24/08/2012 4:51 PM, James Starlight wrote: >> >> up :) >> It's
appeared two additional question...
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Re: [gmx-users] Incorrect bond in top file

[Shima Arasteh]

OK, I checked the bonds section of top, there  is no bond between CN and HN.  

Thanks for it.

But there is a new problem. 

I passed the steps for simulation the protein in water, up to the EM step. I 
ran grompp and then mdrun to do energy minimization. I see the protein broken. 
As you said in another email asked a few hours ago, I ran the command trjconv :
# trjconv -s EM.tpr -f EM.gro -pbc mol -ur compact -o EM_pbc.gro

I still see the protein broken.The FVAL is not connected to the next residue. 
Would you let me know your idea? Is there any trick here?


 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Monday, August 27, 2012 11:08 PM
Subject: Re: [gmx-users] Incorrect bond in top file



On 8/27/12 2:35 PM, Shima Arasteh wrote:
> Please take a look at the .top file generated:
> 
> 
>       1          C      1   FVAL     CN      1      0.357     12.011   ; qtot 
>0.357
>       2         HA      1   FVAL     H1      2        0.1      1.008   ; qtot 
>0.457
>       3          O      1   FVAL     ON      3      -0.51     15.999   ; qtot 
>-0.053
>       4        NH1      1   FVAL      N      4     -0.423     14.007   ; qtot 
>-0.476
>       5          H      1   FVAL     HN      5      0.333      1.008   ; qtot 
>-0.143
>       6        CT1      1   FVAL     CA      6      0.034     12.011   ; qtot 
>-0.109
>       7         HB      1   FVAL     HA      7       0.09      1.008   ; qtot 
>-0.019
>       8        CT1      1   FVAL     CB      8     -0.093     12.011   ; qtot 
>-0.112
>       9         HA      1   FVAL     HB      9       0.09      1.008   ; qtot 
>-0.022
>      10        CT3      1   FVAL    CG1     10     -0.268     12.011   ; qtot 
>-0.29
>      11         HA      1   FVAL   HG11     11       0.09      1.008   ; qtot 
>-0.2
>      12         HA      1   FVAL   HG12     12       0.09      1.008   ; qtot 
>-0.11
>      13         HA      1   FVAL   HG13     13       0.09      1.008   ; qtot 
>-0.02
>      14        CT3      1   FVAL    CG2     14     -0.268     12.011   ; qtot 
>-0.288
>      15         HA      1   FVAL   HG21     15       0.09      1.008   ; qtot 
>-0.198
>      16         HA      1   FVAL   HG22     16       0.09      1.008   ; qtot 
>-0.108
>      17         HA      1   FVAL   HG23     17       0.09      1.008   ; qtot 
>-0.018
>      18          C      1   FVAL      C     18      0.528     12.011   ; qtot 
>0.51
>      19          O      1   FVAL      O     19      -0.51     15.999   ; qtot >0
> ; residue   2 SER rtp SER  q  0.0
>      20        NH1      2    SER      N     20      -0.47     14.007   ; qtot 
>-0.47
> 
> I visualized the .gro file, found CN-HN bond.
> 

What appears in a visualization program is irrelevant.  They all have 
algorithms designed to guess what's connected by distance search, or some 
variation thereof.  What's definitive is the [bonds] section of the topology.  
If that says there is a bond between the two atoms in question, then there's a 
problem.  From the .rtp and .hdb entries, I can see no reason why pdb2gmx would 
make a bond.

-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



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Re: [gmx-users] Incorrect bond in top file

[Justin Lemkul]

On 8/27/12 2:35 PM, Shima Arasteh wrote:

Please take a look at the .top file generated:


  1  C  1   FVAL CN  1  0.357 12.011   ; qtot 
0.357
  2 HA  1   FVAL H1  20.1  1.008   ; qtot 
0.457
  3  O  1   FVAL ON  3  -0.51 15.999   ; qtot 
-0.053
  4NH1  1   FVAL  N  4 -0.423 14.007   ; qtot 
-0.476
  5  H  1   FVAL HN  5  0.333  1.008   ; qtot 
-0.143
  6CT1  1   FVAL CA  6  0.034 12.011   ; qtot 
-0.109
  7 HB  1   FVAL HA  7   0.09  1.008   ; qtot 
-0.019
  8CT1  1   FVAL CB  8 -0.093 12.011   ; qtot 
-0.112
  9 HA  1   FVAL HB  9   0.09  1.008   ; qtot 
-0.022
 10CT3  1   FVALCG1 10 -0.268 12.011   ; qtot 
-0.29
 11 HA  1   FVAL   HG11 11   0.09  1.008   ; qtot 
-0.2
 12 HA  1   FVAL   HG12 12   0.09  1.008   ; qtot 
-0.11
 13 HA  1   FVAL   HG13 13   0.09  1.008   ; qtot 
-0.02
 14CT3  1   FVALCG2 14 -0.268 12.011   ; qtot 
-0.288
 15 HA  1   FVAL   HG21 15   0.09  1.008   ; qtot 
-0.198
 16 HA  1   FVAL   HG22 16   0.09  1.008   ; qtot 
-0.108
 17 HA  1   FVAL   HG23 17   0.09  1.008   ; qtot 
-0.018
 18  C  1   FVAL  C 18  0.528 12.011   ; qtot 
0.51
 19  O  1   FVAL  O 19  -0.51 15.999   ; qtot 0
; residue   2 SER rtp SER  q  0.0
 20NH1  2SER  N 20  -0.47 14.007   ; qtot 
-0.47

I visualized the .gro file, found CN-HN bond.



What appears in a visualization program is irrelevant.  They all have algorithms 
designed to guess what's connected by distance search, or some variation 
thereof.  What's definitive is the [bonds] section of the topology.  If that 
says there is a bond between the two atoms in question, then there's a problem. 
 From the .rtp and .hdb entries, I can see no reason why pdb2gmx would make a bond.


-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


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Re: [gmx-users] Incorrect bond in top file

[Shima Arasteh]

Please take a look at the .top file generated:


 1  C  1   FVAL CN  1  0.357 12.011   ; qtot 
0.357
 2 HA  1   FVAL H1  2    0.1  1.008   ; qtot 
0.457
 3  O  1   FVAL ON  3  -0.51 15.999   ; qtot 
-0.053
 4    NH1  1   FVAL  N  4 -0.423 14.007   ; qtot 
-0.476
 5  H  1   FVAL HN  5  0.333  1.008   ; qtot 
-0.143
 6    CT1  1   FVAL CA  6  0.034 12.011   ; qtot 
-0.109
 7 HB  1   FVAL HA  7   0.09  1.008   ; qtot 
-0.019
 8    CT1  1   FVAL CB  8 -0.093 12.011   ; qtot 
-0.112
 9 HA  1   FVAL HB  9   0.09  1.008   ; qtot 
-0.022
    10    CT3  1   FVAL    CG1 10 -0.268 12.011   ; qtot 
-0.29
    11 HA  1   FVAL   HG11 11   0.09  1.008   ; qtot 
-0.2
    12 HA  1   FVAL   HG12 12   0.09  1.008   ; qtot 
-0.11
    13 HA  1   FVAL   HG13 13   0.09  1.008   ; qtot 
-0.02
    14    CT3  1   FVAL    CG2 14 -0.268 12.011   ; qtot 
-0.288
    15 HA  1   FVAL   HG21 15   0.09  1.008   ; qtot 
-0.198
    16 HA  1   FVAL   HG22 16   0.09  1.008   ; qtot 
-0.108
    17 HA  1   FVAL   HG23 17   0.09  1.008   ; qtot 
-0.018
    18  C  1   FVAL  C 18  0.528 12.011   ; qtot 
0.51
    19  O  1   FVAL  O 19  -0.51 15.999   ; qtot 0
; residue   2 SER rtp SER  q  0.0
    20    NH1  2    SER  N 20  -0.47 14.007   ; qtot 
-0.47

I visualized the .gro file, found CN-HN bond. 


 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Monday, August 27, 2012 10:45 PM
Subject: Re: [gmx-users] Incorrect bond in top file



On 8/27/12 1:31 PM, Shima Arasteh wrote:
> :D
> Hope so ( for your caps lock )! ;)
> Thanks, I'm happy!
>
> The relevant rtp file:
>
>
> [ FVAL ]
>   [ atoms ]
>      CN    C     0.357    0
>      ON    O    -0.51    1
>      H1    HA    0.100    2
>      N    NH1    -0.423    3
>      HN    H    0.333    4
>      CA    CT1    0.034    5
>      HA    HB    0.09    6
>      CB    CT1    -0.093    7
>      HB    HA    0.09    8
>      CG1    CT3    -0.268    9
>      HG11    HA    0.09    10
>      HG12    HA    0.09    11
>      HG13    HA    0.09    12
>      CG2    CT3    -0.268    13
>      HG21    HA    0.09    14
>      HG22    HA    0.09    15
>      HG23    HA    0.09    16
>      C    C    0.528    17
>      O    O    -0.510    18
>   [ bonds ]
>      CN    H1
>      CN    ON
>      CN    N
>      N    HN
>      CA    N
>      CA    HA
>      CA    C
>      C    O
>      CA    CB
>      CB    HB
>      CB    CG1
>      CB    CG2
>      CG2    HG21
>      CG2    HG22
>      CG2    HG23
>      CG1    HG11
>      CG1    HG12
>      CG1    HG13
>
>   [ impropers ]
>      CN     N    ON    H1
>
> The relevant .hdb file:
>
>   FVAL    6
> 1    1    H1    CN    N    ON
> 1    1    HN    N    C    CA
> 1    5    HA    CA    N    C    CB
> 1    5    HB    CB    CA    CG1    CG2
> 3    4    HG1    CG1    CB    CA
> 3    4    HG2    CG2    CB    CA
>

I see nothing out of the ordinary here.  You're saying that HN is bonded to CN 
after running pdb2gmx?

-Justin

>
>
> Sincerely,
> Shima
>
>
> - Original Message -
> From: Justin Lemkul 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users 
> Cc:
> Sent: Monday, August 27, 2012 8:39 PM
> Subject: Re: [gmx-users] Incorrect bond in top file
>
>
>
> On 8/27/12 11:41 AM, Shima Arasteh wrote:
>>
>>
>> Dear users,
>>
>>
>> [ Especially dear Justin ( please don't shout at me! ) ],
>>
>
> I haven't, and won't.  I keep my caps lock off ;)  Hopefully no one gets the
> impression that I have done otherwise...
>
>>
>> As I have described it many times, I defined a new residue named FVAL in 
>> aminoacids.rtp of the force field ( CHARMM36). The first step is "generating 
>> top file". When I ran the command of pdb2gmx, the top file is generated, but 
>> it contains a bond which I have not defined in the FVAL. The incorrect bond 
>> is between H-atom of valine (  this H is one of the atoms connected to the N 
>> of valine and this N is in the backbone, The N of valine is connected to C 
>> of formyl, CA and H)  and C-atom of formyl group! ( It seems that the C of 
>> formyl doesn't form a second ordered bond with O ).
>>
>> aminoacids.hdb and aminoacids.rtp are the files I modified.
>>
>
> Please post the relevant .rtp and .hdb entries.  There is an error somewhere,
> but we can't determine what it is without seeing these.
>
> -Justin
>

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg

Re: [gmx-users] Incorrect bond in top file

[Shima Arasteh]

 Yes. 
So what's the problem?!


Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Monday, August 27, 2012 10:45 PM
Subject: Re: [gmx-users] Incorrect bond in top file



On 8/27/12 1:31 PM, Shima Arasteh wrote:
> :D
> Hope so ( for your caps lock )! ;)
> Thanks, I'm happy!
>
> The relevant rtp file:
>
>
> [ FVAL ]
>   [ atoms ]
>      CN    C     0.357    0
>      ON    O    -0.51    1
>      H1    HA    0.100    2
>      N    NH1    -0.423    3
>      HN    H    0.333    4
>      CA    CT1    0.034    5
>      HA    HB    0.09    6
>      CB    CT1    -0.093    7
>      HB    HA    0.09    8
>      CG1    CT3    -0.268    9
>      HG11    HA    0.09    10
>      HG12    HA    0.09    11
>      HG13    HA    0.09    12
>      CG2    CT3    -0.268    13
>      HG21    HA    0.09    14
>      HG22    HA    0.09    15
>      HG23    HA    0.09    16
>      C    C    0.528    17
>      O    O    -0.510    18
>   [ bonds ]
>      CN    H1
>      CN    ON
>      CN    N
>      N    HN
>      CA    N
>      CA    HA
>      CA    C
>      C    O
>      CA    CB
>      CB    HB
>      CB    CG1
>      CB    CG2
>      CG2    HG21
>      CG2    HG22
>      CG2    HG23
>      CG1    HG11
>      CG1    HG12
>      CG1    HG13
>
>   [ impropers ]
>      CN     N    ON    H1
>
> The relevant .hdb file:
>
>   FVAL    6
> 1    1    H1    CN    N    ON
> 1    1    HN    N    C    CA
> 1    5    HA    CA    N    C    CB
> 1    5    HB    CB    CA    CG1    CG2
> 3    4    HG1    CG1    CB    CA
> 3    4    HG2    CG2    CB    CA
>

I see nothing out of the ordinary here.  You're saying that HN is bonded to CN 
after running pdb2gmx?

-Justin

>
>
> Sincerely,
> Shima
>
>
> - Original Message -
> From: Justin Lemkul 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users 
> Cc:
> Sent: Monday, August 27, 2012 8:39 PM
> Subject: Re: [gmx-users] Incorrect bond in top file
>
>
>
> On 8/27/12 11:41 AM, Shima Arasteh wrote:
>>
>>
>> Dear users,
>>
>>
>> [ Especially dear Justin ( please don't shout at me! ) ],
>>
>
> I haven't, and won't.  I keep my caps lock off ;)  Hopefully no one gets the
> impression that I have done otherwise...
>
>>
>> As I have described it many times, I defined a new residue named FVAL in 
>> aminoacids.rtp of the force field ( CHARMM36). The first step is "generating 
>> top file". When I ran the command of pdb2gmx, the top file is generated, but 
>> it contains a bond which I have not defined in the FVAL. The incorrect bond 
>> is between H-atom of valine (  this H is one of the atoms connected to the N 
>> of valine and this N is in the backbone, The N of valine is connected to C 
>> of formyl, CA and H)  and C-atom of formyl group! ( It seems that the C of 
>> formyl doesn't form a second ordered bond with O ).
>>
>> aminoacids.hdb and aminoacids.rtp are the files I modified.
>>
>
> Please post the relevant .rtp and .hdb entries.  There is an error somewhere,
> but we can't determine what it is without seeing these.
>
> -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


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Re: [gmx-users] Elastic network model -building

[XAvier Periole]

On Aug 27, 2012, at 7:14 PM, mohan maruthi sena wrote:


Hi,
 Thanks for your reply. I have written a script which gives the
atoms with in certain cut-off distance from specified atom. I have
added this to topology , the problem is that it creates topology from
pdb but not the other way.

Not clear what the other way around is!


I use first pdb2gmx -f pdb -o gro -p top (command to generate
gro,top). I use this topology file and add the bonds in this  and use
this topology for further use.  Is this correct,?
I have no idea! It depends what you want to do! Doing like you  
describe you add a elastic network to a atomistic description ... if  
this is not the objective do something that would follow your idea!

,but still i could
not find bonds with other atoms when i load it in vmd. Please suggest
me a way.
VMD defines "default" bonds according to their distances in the  
structure you give. So between Calpha the distance is about 0.38  
nm ... if you use a "dynamic bond" description in VMD and select the  
Calphas ... a cutoff of 4.0 would show you the connections.


Thanks,
Mohan

On Mon, Aug 27, 2012 at 10:29 PM, XAvier Periole   
wrote:


There is no script generating an elastic network in Gromacs.

You could use the script that we developed in the context of the  
Martini CG
model (cgmartini.nl) but it would be certainly easier for you to  
simply
write a script that would rad the Clapha coordinates and define the  
ones
that are within a cut-off distance of your choice and then write a  
list of

bonds that you could add to a gromacs topology file ...


On Aug 26, 2012, at 3:34 PM, mohan maruthi sena wrote:


Hi all,
  I want to build elastic network model for a protein.  To
build an Elastic network model  , I consider only C-alpha atoms of  
the
protein. I want to make c-alpha atoms connect(make bond) with all  
the

other c-alpha atoms , if it falls within certain cut-off distance.
How can i do this?


Please suggest me a way,

Thanks,
Mohan.
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Re: [gmx-users] Incorrect bond in top file

[Justin Lemkul]

On 8/27/12 1:31 PM, Shima Arasteh wrote:

:D
Hope so ( for your caps lock )! ;)
Thanks, I'm happy!

The relevant rtp file:


[ FVAL ]
  [ atoms ]
 CNC 0.3570
 ONO-0.511
 H1HA0.1002
 NNH1-0.4233
 HNH0.3334
 CACT10.0345
 HAHB0.096
 CBCT1-0.0937
 HBHA0.098
 CG1CT3-0.2689
 HG11HA0.0910
 HG12HA0.0911
 HG13HA0.0912
 CG2CT3-0.26813
 HG21HA0.0914
 HG22HA0.0915
 HG23HA0.0916
 CC0.52817
 OO-0.51018
  [ bonds ]
 CNH1
 CNON
 CNN
 NHN
 CAN
 CAHA
 CAC
 CO
 CACB
 CBHB
 CBCG1
 CBCG2
 CG2HG21
 CG2HG22
 CG2HG23
 CG1HG11
 CG1HG12
 CG1HG13

  [ impropers ]
 CN NONH1

The relevant .hdb file:

  FVAL6
11H1CNNON
11HNNCCA
15HACANCCB
15HBCBCACG1CG2
34HG1CG1CBCA
34HG2CG2CBCA



I see nothing out of the ordinary here.  You're saying that HN is bonded to CN 
after running pdb2gmx?


-Justin




Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS users 

Cc:
Sent: Monday, August 27, 2012 8:39 PM
Subject: Re: [gmx-users] Incorrect bond in top file



On 8/27/12 11:41 AM, Shima Arasteh wrote:



Dear users,


[ Especially dear Justin ( please don't shout at me! ) ],



I haven't, and won't.  I keep my caps lock off ;)  Hopefully no one gets the
impression that I have done otherwise...



As I have described it many times, I defined a new residue named FVAL in aminoacids.rtp 
of the force field ( CHARMM36). The first step is "generating top file". When I 
ran the command of pdb2gmx, the top file is generated, but it contains a bond which I 
have not defined in the FVAL. The incorrect bond is between H-atom of valine (  this H is 
one of the atoms connected to the N of valine and this N is in the backbone, The N of 
valine is connected to C of formyl, CA and H)  and C-atom of formyl group! ( It seems 
that the C of formyl doesn't form a second ordered bond with O ).

aminoacids.hdb and aminoacids.rtp are the files I modified.



Please post the relevant .rtp and .hdb entries.  There is an error somewhere,
but we can't determine what it is without seeing these.

-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


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Re: [gmx-users] Force Field Choice

[Justin Lemkul]

On 8/27/12 1:32 PM, Marcelo Depolo wrote:

Dear all,


Is there a consensus on force field choice? I read in this group, people
suggesting compare experimental data and simulation data. But in case of
there's none experimental data about structural data, what to do?



There was a discussion about this just a few days ago, with some good links:

http://lists.gromacs.org/pipermail/gmx-users/2012-August/074205.html

Force fields aren't necessarily balanced against individual proteins, though 
some are used as models.  The only real answer is lots of reading about how the 
force fields were parameterized, along with what their shortcomings and benefits 
are, as have been described in the years over which they've been developed.


-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


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Re: [gmx-users] Incorrect bond in top file

[Shima Arasteh]

:D
Hope so ( for your caps lock )! ;)
Thanks, I'm happy!

The relevant rtp file:


[ FVAL ]
 [ atoms ]
    CN    C     0.357    0
    ON    O    -0.51    1
    H1    HA    0.100    2
    N    NH1    -0.423    3
    HN    H    0.333    4
    CA    CT1    0.034    5
    HA    HB    0.09    6
    CB    CT1    -0.093    7
    HB    HA    0.09    8
    CG1    CT3    -0.268    9
    HG11    HA    0.09    10
    HG12    HA    0.09    11
    HG13    HA    0.09    12
    CG2    CT3    -0.268    13
    HG21    HA    0.09    14
    HG22    HA    0.09    15
    HG23    HA    0.09    16
    C    C    0.528    17
    O    O    -0.510    18
 [ bonds ]
    CN    H1
    CN    ON
    CN    N
    N    HN
    CA    N
    CA    HA
    CA    C
    C    O
    CA    CB
    CB    HB
    CB    CG1
    CB    CG2
    CG2    HG21
    CG2    HG22
    CG2    HG23
    CG1    HG11
    CG1    HG12
    CG1    HG13
     
 [ impropers ]
    CN     N    ON    H1

The relevant .hdb file:

 FVAL    6
1    1    H1    CN    N    ON
1    1    HN    N    C    CA
1    5    HA    CA    N    C    CB
1    5    HB    CB    CA    CG1    CG2
3    4    HG1    CG1    CB    CA
3    4    HG2    CG2    CB    CA



Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Monday, August 27, 2012 8:39 PM
Subject: Re: [gmx-users] Incorrect bond in top file



On 8/27/12 11:41 AM, Shima Arasteh wrote:
>
>
> Dear users,
>
>
> [ Especially dear Justin ( please don't shout at me! ) ],
>

I haven't, and won't.  I keep my caps lock off ;)  Hopefully no one gets the 
impression that I have done otherwise...

>
> As I have described it many times, I defined a new residue named FVAL in 
> aminoacids.rtp of the force field ( CHARMM36). The first step is "generating 
> top file". When I ran the command of pdb2gmx, the top file is generated, but 
> it contains a bond which I have not defined in the FVAL. The incorrect bond 
> is between H-atom of valine (  this H is one of the atoms connected to the N 
> of valine and this N is in the backbone, The N of valine is connected to C of 
> formyl, CA and H)  and C-atom of formyl group! ( It seems that the C of 
> formyl doesn't form a second ordered bond with O ).
>
> aminoacids.hdb and aminoacids.rtp are the files I modified.
>

Please post the relevant .rtp and .hdb entries.  There is an error somewhere, 
but we can't determine what it is without seeing these.

-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



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[gmx-users] Force Field Choice

[Marcelo Depolo]

Dear all,


Is there a consensus on force field choice? I read in this group, people
suggesting compare experimental data and simulation data. But in case of
there's none experimental data about structural data, what to do?

I apologize previously the silly doubt.
Best regards!
-- 
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MSN: marcelodep...@gmail.com 
*Website: http://opensourcebioinformatics.com/site/*
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Re: [gmx-users] Elastic network model -building

[mohan maruthi sena]

Hi,
  Thanks for your reply. I have written a script which gives the
atoms with in certain cut-off distance from specified atom. I have
added this to topology , the problem is that it creates topology from
pdb but not the other way.

I use first pdb2gmx -f pdb -o gro -p top (command to generate
gro,top). I use this topology file and add the bonds in this  and use
this topology for further use.  Is this correct,?,but still i could
not find bonds with other atoms when i load it in vmd. Please suggest
me a way.

Thanks,
Mohan

On Mon, Aug 27, 2012 at 10:29 PM, XAvier Periole  wrote:
>
> There is no script generating an elastic network in Gromacs.
>
> You could use the script that we developed in the context of the Martini CG
> model (cgmartini.nl) but it would be certainly easier for you to simply
> write a script that would rad the Clapha coordinates and define the ones
> that are within a cut-off distance of your choice and then write a list of
> bonds that you could add to a gromacs topology file ...
>
>
> On Aug 26, 2012, at 3:34 PM, mohan maruthi sena wrote:
>
>> Hi all,
>>I want to build elastic network model for a protein.  To
>> build an Elastic network model  , I consider only C-alpha atoms of the
>> protein. I want to make c-alpha atoms connect(make bond) with all the
>> other c-alpha atoms , if it falls within certain cut-off distance.
>> How can i do this?
>>
>>
>> Please suggest me a way,
>>
>> Thanks,
>> Mohan.
>> --
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>
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Re: [gmx-users] Elastic network model -building

[XAvier Periole]

There is no script generating an elastic network in Gromacs.

You could use the script that we developed in the context of the  
Martini CG model (cgmartini.nl) but it would be certainly easier for  
you to simply write a script that would rad the Clapha coordinates and  
define the ones that are within a cut-off distance of your choice and  
then write a list of bonds that you could add to a gromacs topology  
file ...


On Aug 26, 2012, at 3:34 PM, mohan maruthi sena wrote:


Hi all,
   I want to build elastic network model for a protein.  To
build an Elastic network model  , I consider only C-alpha atoms of the
protein. I want to make c-alpha atoms connect(make bond) with all the
other c-alpha atoms , if it falls within certain cut-off distance.
How can i do this?


Please suggest me a way,

Thanks,
Mohan.
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[gmx-users] Question about Multi-level parallelization: MPI and OpenMP

[jesmin jahan]

Dear Gromacs Users,

I have two questions about the multi-level parallelism of Gromacs.
http://www.gromacs.org/Documentation/Acceleration_and_parallelization?highlight=verlet#GPU_acceleration

1. Is this feature is only supported by Gromacs 4.6? Or we can get it
in 4.5.3 also?

2. In Gromacs 4.5.3, I have used OMP_NUM_THREADS=12 mpirun -np 16
mdrun_mpi -s imd.tpr command to run 16 gromacs processes each with 12
threads.

In the log file, I can see

 nodeid: 0  nnodes:  16

Its clear that 16 nodes are being used in work load distribution. But
its not clear whether 12 thread is being used in each of those
processes /nodes because there is no mention about the number of
threads.

Does anyone know about this?

Sincerely.

Jesmin

-- 
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
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[gmx-users] Problem with incorrect GB-Polarization Energy Value

[jesmin jahan]

Dear All,

I am using Gromacs 4.5.3 for GB-Polarization Energy Calculation. As I
am not interested to any other energy terms right now, I have set all
the non-bonded parameters to 0.

I am also calculating GB polarization energy using other available
Molecular Dynamic Packages and doing a comparative study between them
(say: Accuracy Vs. Speed Up).
I have already used Gromacs for calculating GB-energy for 168
different Protein molecules and the energy values reported were more
or less the same as reported by others.

Now, I am using a virus shell as input in this process. It contains
1.5 million atoms. Unfortunately, this time, the energy reported is
almost half of the value reported by others.
So, I am a little bit confused. Am I doing something wrong? I have
heard previously that there is no max size for Gromacs.


If anyone have encountered similar kind of problem or have knowledge
about this, please let me know.

Thanks,
Jesmin



-- 
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PhD Student, CS
Stony Brook University, NY-11790.
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Re: [gmx-users] Incorrect bond in top file

[Justin Lemkul]

On 8/27/12 11:41 AM, Shima Arasteh wrote:



Dear users,


[ Especially dear Justin ( please don't shout at me! ) ],



I haven't, and won't.  I keep my caps lock off ;)  Hopefully no one gets the 
impression that I have done otherwise...




As I have described it many times, I defined a new residue named FVAL in aminoacids.rtp 
of the force field ( CHARMM36). The first step is "generating top file". When I 
ran the command of pdb2gmx, the top file is generated, but it contains a bond which I 
have not defined in the FVAL. The incorrect bond is between H-atom of valine (  this H is 
one of the atoms connected to the N of valine and this N is in the backbone, The N of 
valine is connected to C of formyl, CA and H)  and C-atom of formyl group! ( It seems 
that the C of formyl doesn't form a second ordered bond with O ).

aminoacids.hdb and aminoacids.rtp are the files I modified.



Please post the relevant .rtp and .hdb entries.  There is an error somewhere, 
but we can't determine what it is without seeing these.


-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


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[gmx-users] Incorrect bond in top file

[Shima Arasteh]

Dear users,


[ Especially dear Justin ( please don't shout at me! ) ],


As I have described it many times, I defined a new residue named FVAL in 
aminoacids.rtp of the force field ( CHARMM36). The first step is "generating 
top file". When I ran the command of pdb2gmx, the top file is generated, but it 
contains a bond which I have not defined in the FVAL. The incorrect bond is 
between H-atom of valine (  this H is one of the atoms connected to the N of 
valine and this N is in the backbone, The N of valine is connected to C of 
formyl, CA and H)  and C-atom of formyl group! ( It seems that the C of formyl 
doesn't form a second ordered bond with O ).

aminoacids.hdb and aminoacids.rtp are the files I modified. 


Do you have any suggestions? Please help me. Thanks in advance.
Sincerely,
Shima 
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[gmx-users] RE: Looking for GPU benchmarks

[Mathieu38]

Hi,

 

Thanks for your answer.

 

The thing is that I am a benchmarker and I have no knowledge of the
physics behind GROMACS. My goal is to demonstrate the interest (or not)
in using GPUs for a customer test case.

 

So my idea would be to do one run using the CPU only version of GROMACS,
then modify the input file to add “cutoff-scheme = Verlet” and run the
GPU version.

 

I am not sure how to modify any other parameters without changing the
physics of the problem.

 

Regards,

 

 

Mathieu Dubois

 

Hardware Accelerators expert

Applications & Performances Team

tel : +33 (0)4.76.29.70.56

BULL, Architect of An Open World

http://www.bull.com

 

P Pensez à l’environnement avant d’imprimer / Before printing, think
about the environment.

 

 

 

De : Szilárd Páll [via GROMACS] 
[mailto:Szilárd Páll [via GROMACS]
] 
Envoyé : lundi 27 août 2012 17:26
À : Mathieu38 
Objet : Re: Looking for GPU benchmarks

 


Which system did you run? What settings? 

A few tips: 
- Use CUDA 4.2 (5.0 on Kepler); 
- Have at least 10-20k atoms/GPU (and more to get peak GPU performance);
- Use the shortest cut-off possible to allow CPU-GPU load balancing; 
- Due to initial domain-decomposition/parallelization overhead, 
scaling from one to two GPUs is affected by this overhead. 
(- If load balancing is limited, try using multiple MPI ranks per GPU.) 

-- 
Szilárd 


On Mon, Aug 27, 2012 at 1:31 PM, Mathieu38 <[hidden email]> wrote: 


> I have tried the basic approcah of taking some of the input files that
are 
> provided with the sources of Gromacs or on the website, and adding the
line 
> 
> cutoff-scheme = Verlet 
> 
> in the grompp.mdp file 
> 
> However, I have not find a case where use of GPUs (2 MPI Tasks, 4
OpenMP 
> Threads per MPI tasks, 2 GPUs) lead to a significant speed up,
comparing to 
> a CPU only version using 8 cores on a single node. 
> 
> I don't know if this is because GPU implementation is still not
performant 
> or if this is because my test cases are unappropriate. 
> 
> Any help here would be very much appreciated. 
> 
> Thx 
> 
> 
> 
> 
> -- 
> View this message in context:
http://gromacs.5086.n6.nabble.com/Looking-for-GPU-benchmarks-tp5000377p5
000567.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. 
> -- 
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Re: [gmx-users] Re: Looking for GPU benchmarks

[Szilárd Páll]

Which system did you run? What settings?

A few tips:
- Use CUDA 4.2 (5.0 on Kepler);
- Have at least 10-20k atoms/GPU (and more to get peak GPU performance);
- Use the shortest cut-off possible to allow CPU-GPU load balancing;
- Due to initial domain-decomposition/parallelization overhead,
scaling from one to two GPUs is affected by this overhead.
(- If load balancing is limited, try using multiple MPI ranks per GPU.)

--
Szilárd


On Mon, Aug 27, 2012 at 1:31 PM, Mathieu38  wrote:
> I have tried the basic approcah of taking some of the input files that are
> provided with the sources of Gromacs or on the website, and adding the line
>
> cutoff-scheme = Verlet
>
> in the grompp.mdp file
>
> However, I have not find a case where use of GPUs (2 MPI Tasks, 4 OpenMP
> Threads per MPI tasks, 2 GPUs) lead to a significant speed up, comparing to
> a CPU only version using 8 cores on a single node.
>
> I don't know if this is because GPU implementation is still not performant
> or if this is because my test cases are unappropriate.
>
> Any help here would be very much appreciated.
>
> Thx
>
>
>
>
> --
> View this message in context: 
> http://gromacs.5086.n6.nabble.com/Looking-for-GPU-benchmarks-tp5000377p5000567.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] NPT equilibration in KALP15-DPPC

[Justin Lemkul]

On 8/27/12 10:27 AM, Shima Arasteh wrote:

I removed the water molecules located between carbon chains of lipids. Then updated the 
top file. Should the atom numbers of "nvt.gro"  be changed? This is not clear 
for me.
I updated the nvt.gro,
Running:
grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr

but it gives me an error about one of the atoms in index file!

Or I am supposed to run mdrun without a new grompp?



No.  There are three potential ways to fix this problem (all basically the 
same), depending on when the water molecules entered the bilayer.


1. If water molecules are in the bilayer after system construction, remove them 
even before running EM, modifying the topology and whatever coordinate file you 
have for your non-minimized structure.


2. If the water molecules leak in during NVT, modify nvt.gro and the topology 
and proceed to NPT.


3. Likewise, if water entered during NPT, modify npt.gro and the topology, and 
proceed with more NPT equilibration.


Any modification to the coordinate file requires that the number of atoms in the 
file be updated on the second line.  Thus if you delete two water molecules, the 
number should be accordingly decreased by 6.


-Justin





Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc:
Sent: Monday, August 27, 2012 2:33 PM
Subject: Re: [gmx-users] NPT equilibration in KALP15-DPPC



On 8/27/12 2:30 AM, Shima Arasteh wrote:



Hi,

After the NPT mdrun, I visulized the npt.gro.
I need to know if this npt.gro is the final result of equilibration?


 From mdrun -h:

"The structure file (-c) contains the coordinates and velocities of the last 
step."


I see 2,3 water molecules between the lipid chains. Should I remove them? Can I 
remove them? Or it's not the step that I can make such a decision?



You can remove them.  Update the topology and the number of atoms at the top of
the .gro file, then re-equilibrate.

-Justin


Thanks in advance.

Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS users 

Cc:
Sent: Sunday, August 26, 2012 5:29 PM
Subject: Re: [gmx-users] NPT equilibration in KALP15-DPPC



On 8/26/12 8:54 AM, Shima Arasteh wrote:



Hi,

For NPT equilibration of KALP15 in DPPC following the Justin's tutorial, when
I run the grompp command, I get 4 notes. Is it necessary to pay attention to
the notes ? Are they notable?



Notes are generally notable, yes ;)  Never ignore anything grompp tells you,
that's my rule of thumb.  Some messages are less critical than others.  The ones
shown here are quite important.

These warnings cannot possibly be produced by the .mdp file in the tutorial, and
they suggest that you are not doing NPT under any sort of stable conditions.
You're using plain cutoffs, no constraints, and attempting to produce NVE, which
will surely fail.

-Justin



NOTE 1 [file npt.mdp]: You are using a cut-off for VdW interactions with NVE,
for good energy conservation use vdwtype = Shift (possibly with DispCorr)


NOTE 2 [file npt.mdp]: You are using a cut-off for electrostatics with NVE,
for good energy conservation use coulombtype = PME-Switch or
Reaction-Field-zero

Generated 837 of the 2346 non-bonded parameter combinations Excluding 3
bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours
molecule type 'DPPC' Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'CL'

NOTE 3 [file topol.top, line 929]: The bond in molecule-type Protein between
atoms 4 N and 5 H has an estimated oscillational period of 1.0e-02 ps, which
is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change
the constraints mdp option.

Number of degrees of freedom in T-Coupling group rest is 33897.00

NOTE 4 [file npt.mdp]: You are using a plain Coulomb cut-off, which might
produce artifacts. You might want to consider using PME electrostatics.


Reading Coordinates, Velocities and Box size from old trajectory Will read
whole trajectory Last frame -1 time  100.000 Using frame at t = 100
ps Starting time for run is 0 ps Largest charge group radii for Van der
Waals: 0.239, 0.234 nm Largest charge group radii for Coulomb:   0.239,
0.234 nm This run will generate roughly 1 Mb of data

There were 4 notes

Thanks for your suggestions in advance.

Sincerely, Shima







--


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


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Re: [gmx-users] NPT equilibration in KALP15-DPPC

[Shima Arasteh]

I removed the water molecules located between carbon chains of lipids. Then 
updated the top file. Should the atom numbers of "nvt.gro"  be changed? This is 
not clear for me.
I updated the nvt.gro,
Running:
grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr

but it gives me an error about one of the atoms in index file!

Or I am supposed to run mdrun without a new grompp?



 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Monday, August 27, 2012 2:33 PM
Subject: Re: [gmx-users] NPT equilibration in KALP15-DPPC



On 8/27/12 2:30 AM, Shima Arasteh wrote:
>
>
>   Hi,
>
> After the NPT mdrun, I visulized the npt.gro.
> I need to know if this npt.gro is the final result of equilibration?

From mdrun -h:

"The structure file (-c) contains the coordinates and velocities of the last 
step."

> I see 2,3 water molecules between the lipid chains. Should I remove them? Can 
> I remove them? Or it's not the step that I can make such a decision?
>

You can remove them.  Update the topology and the number of atoms at the top of 
the .gro file, then re-equilibrate.

-Justin

> Thanks in advance.
>
> Sincerely,
> Shima
>
>
> - Original Message -
> From: Justin Lemkul 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users 
> Cc:
> Sent: Sunday, August 26, 2012 5:29 PM
> Subject: Re: [gmx-users] NPT equilibration in KALP15-DPPC
>
>
>
> On 8/26/12 8:54 AM, Shima Arasteh wrote:
>>
>>
>> Hi,
>>
>> For NPT equilibration of KALP15 in DPPC following the Justin's tutorial, when
>> I run the grompp command, I get 4 notes. Is it necessary to pay attention to
>> the notes ? Are they notable?
>>
>
> Notes are generally notable, yes ;)  Never ignore anything grompp tells you,
> that's my rule of thumb.  Some messages are less critical than others.  The 
> ones
> shown here are quite important.
>
> These warnings cannot possibly be produced by the .mdp file in the tutorial, 
> and
> they suggest that you are not doing NPT under any sort of stable conditions.
> You're using plain cutoffs, no constraints, and attempting to produce NVE, 
> which
> will surely fail.
>
> -Justin
>
>>
>> NOTE 1 [file npt.mdp]: You are using a cut-off for VdW interactions with NVE,
>> for good energy conservation use vdwtype = Shift (possibly with DispCorr)
>>
>>
>> NOTE 2 [file npt.mdp]: You are using a cut-off for electrostatics with NVE,
>> for good energy conservation use coulombtype = PME-Switch or
>> Reaction-Field-zero
>>
>> Generated 837 of the 2346 non-bonded parameter combinations Excluding 3
>> bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours
>> molecule type 'DPPC' Excluding 2 bonded neighbours molecule type 'SOL'
>> Excluding 1 bonded neighbours molecule type 'CL'
>>
>> NOTE 3 [file topol.top, line 929]: The bond in molecule-type Protein between
>> atoms 4 N and 5 H has an estimated oscillational period of 1.0e-02 ps, which
>> is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change
>> the constraints mdp option.
>>
>> Number of degrees of freedom in T-Coupling group rest is 33897.00
>>
>> NOTE 4 [file npt.mdp]: You are using a plain Coulomb cut-off, which might
>> produce artifacts. You might want to consider using PME electrostatics.
>>
>>
>> Reading Coordinates, Velocities and Box size from old trajectory Will read
>> whole trajectory Last frame         -1 time  100.000 Using frame at t = 100
>> ps Starting time for run is 0 ps Largest charge group radii for Van der
>> Waals: 0.239, 0.234 nm Largest charge group radii for Coulomb:       0.239,
>> 0.234 nm This run will generate roughly 1 Mb of data
>>
>> There were 4 notes
>>
>> Thanks for your suggestions in advance.
>>
>> Sincerely, Shima
>>
>

-- 


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


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Re: [gmx-users] Re: Cross-correlation maps

[James Starlight]

Mark,

Is there any way to calculate such cross-correlations without
calculation of the covariance matrix ( from the MD trajectory
indirectly) ?
I've noticed that after processind of my trajectory with PCA method
some dynamics ( e.g fluctuations of the side-chains) are lost even
when I've analysed filtered.xtc from the first 50 principal
components. How I should analyse possible cross-correlations of the
fluctuations of the side-chains?

James

2012/8/27 Mark Abraham :
> On 24/08/2012 4:51 PM, James Starlight wrote:
>>
>> up :)
>> It's appeared two additional questions.
>>
>> 1) In addition to the pca's cross-correlation maps I wounder to know
>> about possibility of calculation of such cross-correlation's from the
>> trajectories indirectly without calculation of the covariance
>> matrices.
>>
>> 2) is there any way to calculate degree of fluctuations of side-chains
>> ( degree of  torsion's dynamics) from the different trajectories and
>> to compare it ?
>> E.g I have one protein in two different (apo and holo) forms. I've
>> calculated two trajectories for both structures and observed different
>> degree of dynamics in case of each structure ( e.g fluctuations in
>> case of apo form were  more frequent than in case of liganded form).
>> IS there any way to direct mesure and comprison of such side-chain's
>> dynamics for two trajectories?
>
>
> Yes, but not with GROMACS tools. You can generate a .tpr for use with that
> old version of g_covar with an old version of grompp in a manner similar to
> the way you generate one now, but there are bunch of details different. You
> may not require a .tpr, of course. Look at the file types for g_covar_mod -s
> in the output for -h.
>
> Mark
>
>
>>
>>
>> James
>>
>> 2012/8/15, James Starlight :
>>>
>>> Dear Gromacs users!
>>>
>>>
>>> I want to obtain Cross-correlation maps ( for indication of the
>>> cross-correlated fluctuations of the residues).
>>> The example of such maps can be found here
>>> http://pubs.acs.org/doi/abs/10.1021/ja076046a
>>>
>>>   I found that modificied version of the G_covar from users
>>> contributions can do such things. But because of the older version of
>>> that program (3.3.3) I've obtained the below error using it with 4.5.5
>>> gromacs
>>>
>>>
>>> Reading file md_GO.tpr, VERSION 4.5.5 (single precision)
>>>
>>> ---
>>> Program g_covar_mod, VERSION 3.3.3
>>> Source code file: tpxio.c, line: 1192
>>>
>>> Fatal error:
>>> reading tpx file (md_GO.tpr) version 73 with version 40 program
>>> ---
>>>
>>>
>>> Is there newest versions of the G_covar for such things or
>>> alternativelly any others ways to calculate such correlations maps ?
>>>
>>> Thanks for help
>>>
>>> James
>>>
>
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Re: [gmx-users] GROMACS command for energy calculation

[Mark Abraham]

On 27/08/2012 8:32 PM, Acoot Brett wrote:

Hi Mark,
  
Then MAP file has the ability to recognize the groups saved in the index file, which is in the same folder as the MDP file?


I have no idea what you mean. Make the index groups in the index file 
and use them with commands like grompp -n yourindexfile.ndx -f 
yourparams.mdp


Mark



Acoot


- Original Message -
From: Mark Abraham 
To: Discussion list for GROMACS users 
Cc:
Sent: Monday, 27 August 2012 8:00 PM
Subject: Re: [gmx-users] GROMACS command for energy calculation

On 27/08/2012 7:42 PM, Acoot Brett wrote:

Dear Justin,
For example, I want to calculate the energy between residue 50 and residue 
100, then I create an index file (A), then in the MDP file I will insert 
energygryp=A (with indec file extension or not?), then do the rerun, am I right?

An index file *contains* definitions of index groups. You need an index file 
that defines every group you care about, and you refer to the names of those 
groups in your .mdp file.

Mark


Cheers,
Acoot
 


- Original Message -
From: Justin Lemkul 
To: Acoot Brett ; Discussion list for GROMACS users 

Cc:
Sent: Monday, 27 August 2012 9:53 AM
Subject: Re: [gmx-users] GROMACS command for energy calculation



On 8/26/12 7:44 PM, Acoot Brett wrote:

Dear All,

I am still confused and I hope I can get some detailed explaination. For 
example, I want to determine the interaction energy between residue 52 and 
residue 105, how should I set energyggryp and what is the related commands?

And if I want to determine the interaction energy between residue 52 in China A 
and residue 8 in Chain B, what will be the difference?

You can also tell me a internet link on it.


The help information from make_ndx is what you need.  Type "help" at the prompt
(without quotes) and you will see examples.

For instance, to select residue 52 of chain A:

ch A & r 52

That creates a group that you can then use as an energygrp in the .mdp file.

-Justin


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Re: [gmx-users] Broken protein after EM

[Justin Lemkul]

On 8/27/12 8:27 AM, Shima Arasteh wrote:

Dear gmx users,

I'm simulating a protein in water. I ran these commands:
1.pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter
2.editconf -f monomer.gro -o monomer_newbox.gro -c -d 1.0 -bt cubic
3.genbox -cp monomer_newbox.gro -cs spc216.gro -o monomer_solv.gro -p topol.top
4.grompp -f ions.mdp -c monomer_solv.gro -p topol.top -o ions.tpr
5.genion -s ions.tpr -o monomer_solv_ions.gro -p topol.top -nname CL -nn 1
6.grompp -f EM.mdp -c monomer_solv_ions.gro -p topol.top -o EM.tpr
7.mdrun -v -deffnm EM

Up to step 7 everything is normal. When I run the 7th command and then 
visualize the product of EM, the protein is broken into 3 distinct parts. Would 
you please give me your suggestions to solve?
Is PBC may be the reason of such problem?



It usually is.  For simple protein-in-water systems, try:

trjconv -s EM.tpr -f EM.gro -pbc mol -ur compact -o EM_pbc.gro

Should do the trick.

-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


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[gmx-users] Broken protein after EM

[Shima Arasteh]

Dear gmx users,

I'm simulating a protein in water. I ran these commands:
1.pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter
2.editconf -f monomer.gro -o monomer_newbox.gro -c -d 1.0 -bt cubic
3.genbox -cp monomer_newbox.gro -cs spc216.gro -o monomer_solv.gro -p topol.top
4.grompp -f ions.mdp -c monomer_solv.gro -p topol.top -o ions.tpr
5.genion -s ions.tpr -o monomer_solv_ions.gro -p topol.top -nname CL -nn 1
6.grompp -f EM.mdp -c monomer_solv_ions.gro -p topol.top -o EM.tpr
7.mdrun -v -deffnm EM

Up to step 7 everything is normal. When I run the 7th command and then 
visualize the product of EM, the protein is broken into 3 distinct parts. Would 
you please give me your suggestions to solve?
Is PBC may be the reason of such problem? 


Thanks in advance.
Sincerely,
Shima
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[gmx-users] Variation of box angles - regd

[ramesh cheerla]

Dear GMX users,

 I  want to see how box angles are
varying during  my simulations,  I have no idea where box angles will
be stored in gromacs output files and how  to extract them .   Can
anybody  please help me in this regard.



Thank you in advance


Regards,
Ramesh.
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Re: [gmx-users] Re: Looking for GPU benchmarks

[Justin Lemkul]

On 8/27/12 7:31 AM, Mathieu38 wrote:

I have tried the basic approcah of taking some of the input files that are
provided with the sources of Gromacs or on the website, and adding the line

cutoff-scheme = Verlet

in the grompp.mdp file

However, I have not find a case where use of GPUs (2 MPI Tasks, 4 OpenMP
Threads per MPI tasks, 2 GPUs) lead to a significant speed up, comparing to
a CPU only version using 8 cores on a single node.

I don't know if this is because GPU implementation is still not performant
or if this is because my test cases are unappropriate.

Any help here would be very much appreciated.



Have you pulled the correct development branch from the git repository?  The 
changes have not yet been merged into the release-4-6 branch, as they are still 
pending in the Gerrit review system.  If you're working with any of the source 
distributions from the website, those will not work.


-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


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[gmx-users] Re: [gmx-developers] Mails rejected with "The message's content type was not explicitly allowed"

[Rossen Apostolov]

Hi,

There was an issue with /multipart/ missing from the allowed mime types. 
Now HTML mails should be also accepted.


Rossen

On 7/5/12 3:24 PM, Rossen Apostolov wrote:

Dear all,

Recently the Gromacs mailing lists have been used for sending spam and 
viruses, and thus now only plain text messages are accepted.


If you have received rejected mails saying "The message's content type 
was not explicitly allowed" it means that you have used in your mail 
special styles or formatting (e.g. bold typeface, colors etc.).


Check your email client settings about how to send messages as plain 
text, e.g. in GMail make sure to click on "Compose -> Plain Text". 
Check also whether a formatted signature is added.


Attachments are also not allowed but you could include links for 
downloads.


Rossen




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[gmx-users] Re: Looking for GPU benchmarks

[Mathieu38]

I have tried the basic approcah of taking some of the input files that are 
provided with the sources of Gromacs or on the website, and adding the line 

cutoff-scheme = Verlet 

in the grompp.mdp file 

However, I have not find a case where use of GPUs (2 MPI Tasks, 4 OpenMP 
Threads per MPI tasks, 2 GPUs) lead to a significant speed up, comparing to 
a CPU only version using 8 cores on a single node. 

I don't know if this is because GPU implementation is still not performant 
or if this is because my test cases are unappropriate. 

Any help here would be very much appreciated. 

Thx 




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[gmx-users] test, please ignore

[Rossen Apostolov]

test
*test*
/test/
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Re: [gmx-users] overlaps atoms during solvation(genbox)

[Justin Lemkul]

On 8/27/12 6:47 AM, Vasumathi Velachi wrote:

Hi

I new in using Gromacs.

I used genbox to solvate my solute(gold+thiols), when I am doing so the
resultant pdb have the overlaps between water molecule and gold. This overlaps
is due to the missing information for gold in the file "vdwdradii.dat". In order
to avoid the overlaps shall i increase vdwd radii while solvating or shall  I
include the vdwd radii information for gold atoms in "vdwdradii.dat" file.



The most straightforward solution is to add an entry for gold in vdwradii.dat. 
Make a local copy of the file in the working directory and make your modifications.


-Justin

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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


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[gmx-users] overlaps atoms during solvation(genbox)

[Vasumathi Velachi]

Hi

I new in using Gromacs.

I used genbox to solvate my solute(gold+thiols), when I am doing so the 
resultant pdb have the overlaps between water molecule and gold. This 
overlaps is due to the missing information for gold in the file 
"vdwdradii.dat". In order to avoid the overlaps shall i increase vdwd 
radii while solvating or shall  I include the vdwd radii information for 
gold atoms in "vdwdradii.dat" file.


Thanking you in advance



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Vasumathi Velachi


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Re: [gmx-users] GROMACS command for energy calculation

[Justin Lemkul]

On 8/27/12 6:32 AM, Acoot Brett wrote:

Hi Mark,

Then MAP file has the ability to recognize the groups saved in the index file, 
which is in the same folder as the MDP file?



Any group specified in the .mdp file must be recognized by grompp (in the case 
of default groups) or otherwise supplied by the user via an index file passed to 
the -n flag of grompp.  It is not necessarily automatically recognized and can 
be in any location you like.


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

-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


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Re: [gmx-users] GROMACS command for energy calculation

[Acoot Brett]

Hi Mark,
 
Then MAP file has the ability to recognize the groups saved in the index file, 
which is in the same folder as the MDP file? 

Acoot


- Original Message -
From: Mark Abraham 
To: Discussion list for GROMACS users 
Cc: 
Sent: Monday, 27 August 2012 8:00 PM
Subject: Re: [gmx-users] GROMACS command for energy calculation

On 27/08/2012 7:42 PM, Acoot Brett wrote:
> Dear Justin,
>   For example, I want to calculate the energy between residue 50 and residue 
>100, then I create an index file (A), then in the MDP file I will insert 
>energygryp=A (with indec file extension or not?), then do the rerun, am I 
>right?

An index file *contains* definitions of index groups. You need an index file 
that defines every group you care about, and you refer to the names of those 
groups in your .mdp file.

Mark

>   Cheers,
>   Acoot
>    
> 
> - Original Message -
> From: Justin Lemkul 
> To: Acoot Brett ; Discussion list for GROMACS users 
> 
> Cc:
> Sent: Monday, 27 August 2012 9:53 AM
> Subject: Re: [gmx-users] GROMACS command for energy calculation
> 
> 
> 
> On 8/26/12 7:44 PM, Acoot Brett wrote:
>> Dear All,
>> 
>> I am still confused and I hope I can get some detailed explaination. For 
>> example, I want to determine the interaction energy between residue 52 and 
>> residue 105, how should I set energyggryp and what is the related commands?
>> 
>> And if I want to determine the interaction energy between residue 52 in 
>> China A and residue 8 in Chain B, what will be the difference?
>> 
>> You can also tell me a internet link on it.
>> 
> The help information from make_ndx is what you need.  Type "help" at the 
> prompt
> (without quotes) and you will see examples.
> 
> For instance, to select residue 52 of chain A:
> 
> ch A & r 52
> 
> That creates a group that you can then use as an energygrp in the .mdp file.
> 
> -Justin
> 

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Re: [gmx-users] NPT equilibration in KALP15-DPPC

[Justin Lemkul]

On 8/27/12 2:30 AM, Shima Arasteh wrote:



  Hi,

After the NPT mdrun, I visulized the npt.gro.
I need to know if this npt.gro is the final result of equilibration?


From mdrun -h:

"The structure file (-c) contains the coordinates and velocities of the last 
step."


I see 2,3 water molecules between the lipid chains. Should I remove them? Can I 
remove them? Or it's not the step that I can make such a decision?



You can remove them.  Update the topology and the number of atoms at the top of 
the .gro file, then re-equilibrate.


-Justin


Thanks in advance.

Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS users 

Cc:
Sent: Sunday, August 26, 2012 5:29 PM
Subject: Re: [gmx-users] NPT equilibration in KALP15-DPPC



On 8/26/12 8:54 AM, Shima Arasteh wrote:



Hi,

For NPT equilibration of KALP15 in DPPC following the Justin's tutorial, when
I run the grompp command, I get 4 notes. Is it necessary to pay attention to
the notes ? Are they notable?



Notes are generally notable, yes ;)  Never ignore anything grompp tells you,
that's my rule of thumb.  Some messages are less critical than others.  The ones
shown here are quite important.

These warnings cannot possibly be produced by the .mdp file in the tutorial, and
they suggest that you are not doing NPT under any sort of stable conditions.
You're using plain cutoffs, no constraints, and attempting to produce NVE, which
will surely fail.

-Justin



NOTE 1 [file npt.mdp]: You are using a cut-off for VdW interactions with NVE,
for good energy conservation use vdwtype = Shift (possibly with DispCorr)


NOTE 2 [file npt.mdp]: You are using a cut-off for electrostatics with NVE,
for good energy conservation use coulombtype = PME-Switch or
Reaction-Field-zero

Generated 837 of the 2346 non-bonded parameter combinations Excluding 3
bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours
molecule type 'DPPC' Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'CL'

NOTE 3 [file topol.top, line 929]: The bond in molecule-type Protein between
atoms 4 N and 5 H has an estimated oscillational period of 1.0e-02 ps, which
is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change
the constraints mdp option.

Number of degrees of freedom in T-Coupling group rest is 33897.00

NOTE 4 [file npt.mdp]: You are using a plain Coulomb cut-off, which might
produce artifacts. You might want to consider using PME electrostatics.


Reading Coordinates, Velocities and Box size from old trajectory Will read
whole trajectory Last frame -1 time  100.000 Using frame at t = 100
ps Starting time for run is 0 ps Largest charge group radii for Van der
Waals: 0.239, 0.234 nm Largest charge group radii for Coulomb:   0.239,
0.234 nm This run will generate roughly 1 Mb of data

There were 4 notes

Thanks for your suggestions in advance.

Sincerely, Shima





--


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


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Re: [gmx-users] GROMACS command for energy calculation

[Mark Abraham]

On 27/08/2012 7:42 PM, Acoot Brett wrote:

Dear Justin,
  
For example, I want to calculate the energy between residue 50 and residue 100, then I create an index file (A), then in the MDP file I will insert energygryp=A (with indec file extension or not?), then do the rerun, am I right?


An index file *contains* definitions of index groups. You need an index 
file that defines every group you care about, and you refer to the names 
of those groups in your .mdp file.


Mark

  
Cheers,
  
Acoot
  
  



- Original Message -
From: Justin Lemkul 
To: Acoot Brett ; Discussion list for GROMACS users 

Cc:
Sent: Monday, 27 August 2012 9:53 AM
Subject: Re: [gmx-users] GROMACS command for energy calculation



On 8/26/12 7:44 PM, Acoot Brett wrote:

Dear All,

I am still confused and I hope I can get some detailed explaination. For 
example, I want to determine the interaction energy between residue 52 and 
residue 105, how should I set energyggryp and what is the related commands?

And if I want to determine the interaction energy between residue 52 in China A 
and residue 8 in Chain B, what will be the difference?

You can also tell me a internet link on it.


The help information from make_ndx is what you need.  Type "help" at the prompt
(without quotes) and you will see examples.

For instance, to select residue 52 of chain A:

ch A & r 52

That creates a group that you can then use as an energygrp in the .mdp file.

-Justin



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Re: [gmx-users] GROMACS command for energy calculation

[Acoot Brett]

Dear Justin,
 
For example, I want to calculate the energy between residue 50 and residue 100, 
then I create an index file (A), then in the MDP file I will insert 
energygryp=A (with indec file extension or not?), then do the rerun, am I right?
 
Cheers,
 
Acoot
 
 


- Original Message -
From: Justin Lemkul 
To: Acoot Brett ; Discussion list for GROMACS users 

Cc: 
Sent: Monday, 27 August 2012 9:53 AM
Subject: Re: [gmx-users] GROMACS command for energy calculation



On 8/26/12 7:44 PM, Acoot Brett wrote:
> Dear All,
>
> I am still confused and I hope I can get some detailed explaination. For 
> example, I want to determine the interaction energy between residue 52 and 
> residue 105, how should I set energyggryp and what is the related commands?
>
> And if I want to determine the interaction energy between residue 52 in China 
> A and residue 8 in Chain B, what will be the difference?
>
> You can also tell me a internet link on it.
>

The help information from make_ndx is what you need.  Type "help" at the prompt 
(without quotes) and you will see examples.

For instance, to select residue 52 of chain A:

ch A & r 52

That creates a group that you can then use as an energygrp in the .mdp file.

-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


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