Re: [gmx-users] Re: g_analyze

[bharat gupta]

thank you informing about g_rdf...

Is it possible to dump the structure with those average water molecules
interacting with the residues. I generated the hbond.log file which gives
the details but I need to generate a figure for this ??


On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul  wrote:

>
>
> On 11/10/13 8:38 PM, bharat gupta wrote:
>
>> But trjorder can be used to calculate the hydration layer or shell around
>> residues ... Right ??
>>
>>
> Yes, but I also tend to think that integrating an RDF is also a more
> straightforward way of doing that.  With trjorder, you set some arbitrary
> cutoff that may or may not be an informed decision - with an RDF it is
> clear where the hydration layers are.
>
> -Justin
>
>
>
>> On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 11/10/13 8:30 PM, bharat gupta wrote:
>>>
>>>  Thanks for your reply. I was missing the scientific notation part. Now
 everything is fine.

 Regarding trjorder, it doesn't measure h-bonds but gives the water
 nearest
 to protein.


  I wouldn't try to draw any sort of comparison between the output of
>>> trjorder and g_hbond.  If you want to measure H-bonds, there's only one
>>> tool for that.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>>
>>> ==
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
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>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
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Re: [gmx-users] Re: g_analyze

[Justin Lemkul]

On 11/10/13 8:38 PM, bharat gupta wrote:

But trjorder can be used to calculate the hydration layer or shell around
residues ... Right ??



Yes, but I also tend to think that integrating an RDF is also a more 
straightforward way of doing that.  With trjorder, you set some arbitrary cutoff 
that may or may not be an informed decision - with an RDF it is clear where the 
hydration layers are.


-Justin



On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul  wrote:




On 11/10/13 8:30 PM, bharat gupta wrote:


Thanks for your reply. I was missing the scientific notation part. Now
everything is fine.

Regarding trjorder, it doesn't measure h-bonds but gives the water nearest
to protein.



I wouldn't try to draw any sort of comparison between the output of
trjorder and g_hbond.  If you want to measure H-bonds, there's only one
tool for that.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Re: [gmx-users] Re: g_analyze

[bharat gupta]

But trjorder can be used to calculate the hydration layer or shell around
residues ... Right ??


On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul  wrote:

>
>
> On 11/10/13 8:30 PM, bharat gupta wrote:
>
>> Thanks for your reply. I was missing the scientific notation part. Now
>> everything is fine.
>>
>> Regarding trjorder, it doesn't measure h-bonds but gives the water nearest
>> to protein.
>>
>>
> I wouldn't try to draw any sort of comparison between the output of
> trjorder and g_hbond.  If you want to measure H-bonds, there's only one
> tool for that.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Re: g_analyze

[Justin Lemkul]

On 11/10/13 8:30 PM, bharat gupta wrote:

Thanks for your reply. I was missing the scientific notation part. Now
everything is fine.

Regarding trjorder, it doesn't measure h-bonds but gives the water nearest
to protein.



I wouldn't try to draw any sort of comparison between the output of trjorder and 
g_hbond.  If you want to measure H-bonds, there's only one tool for that.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Re: g_analyze

[bharat gupta]

Thanks for your reply. I was missing the scientific notation part. Now
everything is fine.

Regarding trjorder, it doesn't measure h-bonds but gives the water nearest
to protein.




On Mon, Nov 11, 2013 at 10:12 AM, Justin Lemkul  wrote:

>
>
> On 11/10/13 7:18 PM, bharat gupta wrote:
>
>> I checked the file hbnum.xvg file and it contains three columns - time,
>> hbonds, hbonds that donot follow the angle criteria. In that case SS1 is
>>
>
> The third column is not actually H-bonds, then ;)
>
>
>  the average of actual hbonds (2nd column ) and SS2 is the average of 3rd
>> column. Am I right here or not ??
>>
>>
> Yes.
>
>
>  I tried to calculate the h-bond for residues 115-118 individually, and
>> then
>> checked the average for each residue. For single residue calculation, the
>> g_analyze average value is correct.
>>
>> But when I calculate the h-bond as a range 115-118, I get the g_analyze
>> value as 1.62 . I calculated the average manually in excel, got the
>> average
>> values as 16.2 [which is (g_analyze avg value)/10].
>>
>>
> That is impossible.  You cannot get a different average by examining the
> same numbers.  Read the g_analyze output again - I am willing to bet that
> you're not seeing the exponent of the scientific notation.
>
>
>  I then added up the average values of h-bonds of individual residues and
>> the final comes around 16.2, same as that of the 115-118 range h-bonds.
>> This means that my calculation is correct.
>>
>> I also used trjorder to calculate h-bond at distance 0.34 for residues
>> 115-118. I got the average value around 2.51 from g_analyze, where as
>> manual calculation gives 25.1. I don't knw why for the range the g_analyze
>> give avg as (actual avg value)/10 ??
>>
>> Why does trjorder and g_hbond gives different number of hydrogen bonds for
>> the same residue set??
>>
>>
> All of this comes down to correctly reading the screen output.  I have no
> idea what you're doing with trjorder, though.  It doesn't measure H-bonds.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
> --
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Re: [gmx-users] Re: g_analyze

[Justin Lemkul]

On 11/10/13 7:18 PM, bharat gupta wrote:

I checked the file hbnum.xvg file and it contains three columns - time,
hbonds, hbonds that donot follow the angle criteria. In that case SS1 is


The third column is not actually H-bonds, then ;)


the average of actual hbonds (2nd column ) and SS2 is the average of 3rd
column. Am I right here or not ??



Yes.


I tried to calculate the h-bond for residues 115-118 individually, and then
checked the average for each residue. For single residue calculation, the
g_analyze average value is correct.

But when I calculate the h-bond as a range 115-118, I get the g_analyze
value as 1.62 . I calculated the average manually in excel, got the average
values as 16.2 [which is (g_analyze avg value)/10].



That is impossible.  You cannot get a different average by examining the same 
numbers.  Read the g_analyze output again - I am willing to bet that you're not 
seeing the exponent of the scientific notation.



I then added up the average values of h-bonds of individual residues and
the final comes around 16.2, same as that of the 115-118 range h-bonds.
This means that my calculation is correct.

I also used trjorder to calculate h-bond at distance 0.34 for residues
115-118. I got the average value around 2.51 from g_analyze, where as
manual calculation gives 25.1. I don't knw why for the range the g_analyze
give avg as (actual avg value)/10 ??

Why does trjorder and g_hbond gives different number of hydrogen bonds for
the same residue set??



All of this comes down to correctly reading the screen output.  I have no idea 
what you're doing with trjorder, though.  It doesn't measure H-bonds.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Re: Thankful

[Williams Ernesto Miranda Delgado]

Justin, thank you very much for your kind help about LIE and PME
Williams

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Re: [gmx-users] Re: g_analyze

[bharat gupta]

I checked the file hbnum.xvg file and it contains three columns - time,
hbonds, hbonds that donot follow the angle criteria. In that case SS1 is
the average of actual hbonds (2nd column ) and SS2 is the average of 3rd
column. Am I right here or not ??

I tried to calculate the h-bond for residues 115-118 individually, and then
checked the average for each residue. For single residue calculation, the
g_analyze average value is correct.

But when I calculate the h-bond as a range 115-118, I get the g_analyze
value as 1.62 . I calculated the average manually in excel, got the average
values as 16.2 [which is (g_analyze avg value)/10].

I then added up the average values of h-bonds of individual residues and
the final comes around 16.2, same as that of the 115-118 range h-bonds.
This means that my calculation is correct.

I also used trjorder to calculate h-bond at distance 0.34 for residues
115-118. I got the average value around 2.51 from g_analyze, where as
manual calculation gives 25.1. I don't knw why for the range the g_analyze
give avg as (actual avg value)/10 ??

Why does trjorder and g_hbond gives different number of hydrogen bonds for
the same residue set??

Thanks
---
BHARAT



On Sun, Nov 10, 2013 at 10:01 PM, Justin Lemkul  wrote:

>
>
> On 11/10/13 12:20 AM, bharat gupta wrote:
>
>> Hi,
>> I used the command g_hbond to find h-bond between  residues 115-118 and
>> water. Then I used g_analyze to find out the average and it gives the
>> value
>> for the hbonds like this :-
>>
>>std. dev.relative deviation of
>> standard   -   cumulants from those of
>> set  average   deviation  sqrt(n-1)   a Gaussian distribition
>>cum. 3   cum. 4
>> SS1   6.877249e-02   2.546419e-01   5.092839e-03   2.1813.495
>> SS2   6.997201e-02   2.673450e-01   5.346901e-03   2.4215.001
>>
>> When I calculated the average manually, by taking the average of numbers
>> in
>> second column of hbnum.xvg file, I got a value of around 13.5.. What is
>> the
>> reason for such a large difference.
>>
>>
> Hard to say, but I've never known g_analyze to be wrong, so I'd suspect
> something is amiss in your manual calculation.  The difference between 13.5
> and 0.0069 is huge; you should be able to scan through the data file to see
> what the expected value should be.
>
>
>  In another case, g_analyze gives avg values of aroun 6.9 for hbond between
>> two residues and when I calculated it maually I got the avg values as 6.8
>>
>>> ..
>>>
>>
>> Whats the meaning of SS1 and SS2,?? Does it mean that SS1 refers to time
>> and SS2 refers to hbond numbers in the hbnum.xvg obtained from g_hbond
>> analysis ??
>>
>
> Data sets 1 and 2.  You will note that there are two columns of data in
> the -hbnum output produced by g_hbond, with titles explaining both.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
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[gmx-users] Bilayer COM removal issue: Large VCM

[rajat desikan]

Hi All,
I am experiencing a few problems in membrane simulations wrt COM removal. I
downloaded a 400 ns pre-equilibrated Slipid-DMPC membrane with all the
accompanying files. I then carried out the following steps:
1) energy minimization
2) NVT Eq - 100 ps
3) NPT Eq - 250 ps (Berendsen temp, Pres coupling)

Then I used g_select to select the upper and lower DMPC leaflets. The then
carried out a 250 ps NPT eq again. The only change was:
comm-grps= SOL DMPC ==>comm-grps
= SOL upper lower

On every step in log file, I get the following message:













*Step   Time Lambda 124000
248.00.0Large VCM(group lower): -0.00051,
-0.00515, -0.00652, Temp-cm:  8.11828e+29   Energies
(kJ/mol)U-BProper Dih.  Improper Dih.  LJ-14
Coulomb-147.23818e+044.19778e+046.46641e+024.54801e+03
-1.45245e+05LJ (SR)LJ (LR)  Disper. corr.   Coulomb (SR)
Coul. recip.2.79689e+04   -3.78407e+03   -2.10679e+03   -5.84134e+05
-8.87497e+04  PotentialKinetic En.   Total EnergyTemperature
Pres. DC (bar)   -6.76497e+051.76468e+05   -5.00029e+05
3.10424e+02   -1.05704e+02 Pressure (bar)   Constr. rmsd   -1.85927e+02
6.42934e-06*









*Large VCM(group lower): -0.00187, -0.00369,  0.00032,
Temp-cm:  2.02076e+29Large VCM(group lower): -0.00725,
-0.00278, -0.00549, Temp-cm:  1.05988e+30Large VCM(group lower):
0.00020,  0.00308, -0.00176, Temp-cm:  1.48126e+29Large VCM(group
lower): -0.00541,  0.00546, -0.00166, Temp-cm:
7.24656e+29Large VCM(group lower): -0.00220,  0.00362,
-0.00741, Temp-cm:  8.53812e+29Large VCM(group lower):  0.00140,
-0.00160,  0.00029, Temp-cm:  5.39679e+28Large VCM(group lower):
-0.00056, -0.00293, -0.00364, Temp-cm:  2.59422e+29Large VCM(group
lower): -0.00172, -0.00260,  0.00494, Temp-cm:
3.99945e+29Large VCM(group lower):  0.00252,  0.00594,
0.00068, Temp-cm:  4.93342e+29*
*DD  step 124999  vol min/aver 0.702  load imb.: force  1.3%  pme
mesh/force 0.636*

I do not know what to make of it. There are no issues when I remove COM for
the entire system. I have seen this issue come up a few times in the
archives too, but I didn't find a satisfactory solution since the bilayer
was very well equilibrated.

I would appreciate any suggestions. Thank you.


-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] Umbrella Sampling tutorial

[Justin Lemkul]

On 11/10/13 9:14 AM, shahab shariati wrote:

Dear Justin

Very thanks for your reply.


What you described earlier should not be attempted with "distance"
geometry. It won't work very well. The use of restraints is almost
NEVER necessary, especially in the case where the reference group > is

much more massive than the pulling group.

I want to calculate Potential of mean force as a function of the distance
between the centers of mass of drug and the lipid bilayer.

You said distance geometry won't work very well in my case.

What is your better suggestion about my case?



http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html

pull_geometry = position

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Umbrella Sampling tutorial

[shahab shariati]

Dear Justin

Very thanks for your reply.

> What you described earlier should not be attempted with "distance"
> geometry. It won't work very well. The use of restraints is almost
> NEVER necessary, especially in the case where the reference group > is
much more massive than the pulling group.

I want to calculate Potential of mean force as a function of the distance
between the centers of mass of drug and the lipid bilayer.

You said distance geometry won't work very well in my case.

What is your better suggestion about my case?

Best wishes
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Re: [gmx-users] problem in running mdrun command

[Mark Abraham]

Hi,

There's nothing GROMACS-specific here - something about your MPI
installation, configuration or use is pretty wrong, but we can't help work
out what.

Mark


On Sun, Nov 10, 2013 at 12:31 PM, S.Chandra Shekar <
chandrashe...@iisertvm.ac.in> wrote:

> Dear all
>
> I encounter a problem while running command  mdrun_mpi -v -deffnm em in
> gromacs.
>
> I am new to the gromacs. i just ran test calculation, *simulation of
> lyzozyme in water*. i am able to generate gro, tpr files. But in the final
> step i got following error.
>
>  Thanks in advance.
>
>
> [localhost.localdomain:23122] mca: base: component_find: paffinity
> "mca_paffinity_linux" uses an MCA interface that is not recognized
> (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored
> [localhost.localdomain:23123] mca: base: component_find: paffinity
> "mca_paffinity_linux" uses an MCA interface that is not recognized
> (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored
> [localhost.localdomain:23123] mca: base: component_find: ras
> "mca_ras_dash_host" uses an MCA interface that is not recognized (component
> MCA v1.0.0 != supported MCA v2.0.0) -- ignored
> [localhost.localdomain:23123] mca: base: component_find: ras
> "mca_ras_gridengine" uses an MCA interface that is not recognized
> (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored
> [localhost.localdomain:23123] mca: base: component_find: ras
> "mca_ras_localhost" uses an MCA interface that is not recognized (component
> MCA v1.0.0 != supported MCA v2.0.0) -- ignored
> [localhost.localdomain:23123] mca: base: component_find: errmgr
> "mca_errmgr_hnp" uses an MCA interface that is not recognized (component
> MCA v1.0.0 != supported MCA v2.0.0) -- ignored
> [localhost.localdomain:23123] mca: base: component_find: errmgr
> "mca_errmgr_orted" uses an MCA interface that is not recognized (component
> MCA v1.0.0 != supported MCA v2.0.0) -- ignored
> [localhost.localdomain:23123] mca: base: component_find: errmgr
> "mca_errmgr_proxy" uses an MCA interface that is not recognized (component
> MCA v1.0.0 != supported MCA v2.0.0) -- ignored
> [localhost.localdomain:23123] mca: base: component_find: iof
> "mca_iof_proxy" uses an MCA interface that is not recognized (component MCA
> v1.0.0 != supported MCA v2.0.0) -- ignored
> [localhost.localdomain:23123] mca: base: component_find: iof "mca_iof_svc"
> uses an MCA interface that is not recognized (component MCA v1.0.0 !=
> supported MCA v2.0.0) -- ignored
> [localhost.localdomain:23122] mca: base: component_find: rcache
> "mca_rcache_rb" uses an MCA interface that is not recognized (component MCA
> v1.0.0 != supported MCA v2.0.0) -- ignored
> [localhost:23122] *** Process received signal ***
> [localhost:23122] Signal: Segmentation fault (11)
> [localhost:23122] Signal code: Address not mapped (1)
> [localhost:23122] Failing at address: 0x4498
> [localhost:23122] [ 0] /lib64/libpthread.so.0() [0x3fcee0f500]
> [localhost:23122] [ 1] /usr/local/lib/libmpi.so.1(PMPI_Comm_size+0x4e)
> [0x2acc6d93727e]
> [localhost:23122] [ 2]
> /usr/local/gromacs/bin/../lib/libgmx_mpi.so.8(gmx_setup+0x32)
> [0x2acc6d195e02]
> [localhost:23122] [ 3]
> /usr/local/gromacs/bin/../lib/libgmx_mpi.so.8(init_par+0x51)
> [0x2acc6d234251]
> [localhost:23122] [ 4] mdrun_mpi(cmain+0x11f9) [0x435799]
> [localhost:23122] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd)
> [0x3fcea1ecdd]
> [localhost:23122] [ 6] mdrun_mpi() [0x406ee9]
> [localhost:23122] *** End of error message ***
> Segmentation fault (core dumped)
> --
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Re: [gmx-users] Umbrella Sampling tutorial

[Justin Lemkul]

On 11/10/13 5:31 AM, shahab shariati wrote:

Dear Justin

Thanks for your reply.

You are right. I should  not extrapolate too literally from your tutorial
to my system.

But, I have a general question:

There is 2 groups in COM pulling method (reference group + pull group).

If I want to use pull_geometry = distance, so, I should fix reference group
to be immobile. Is it true?



What you described earlier should not be attempted with "distance" geometry.  It 
won't work very well.  The use of restraints is almost NEVER necessary, 
especially in the case where the reference group is much more massive than the 
pulling group.



On the other hand, I want to know exactly using position restraining on
reference group is optional or mandatory in COM pulling method?



Almost never used.  More explicitly - you do not need position restraints.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Re: g_analyze

[Justin Lemkul]

On 11/10/13 12:20 AM, bharat gupta wrote:

Hi,
I used the command g_hbond to find h-bond between  residues 115-118 and
water. Then I used g_analyze to find out the average and it gives the value
for the hbonds like this :-

   std. dev.relative deviation of
standard   -   cumulants from those of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
   cum. 3   cum. 4
SS1   6.877249e-02   2.546419e-01   5.092839e-03   2.1813.495
SS2   6.997201e-02   2.673450e-01   5.346901e-03   2.4215.001

When I calculated the average manually, by taking the average of numbers in
second column of hbnum.xvg file, I got a value of around 13.5.. What is the
reason for such a large difference.



Hard to say, but I've never known g_analyze to be wrong, so I'd suspect 
something is amiss in your manual calculation.  The difference between 13.5 and 
0.0069 is huge; you should be able to scan through the data file to see what the 
expected value should be.



In another case, g_analyze gives avg values of aroun 6.9 for hbond between
two residues and when I calculated it maually I got the avg values as 6.8

..


Whats the meaning of SS1 and SS2,?? Does it mean that SS1 refers to time
and SS2 refers to hbond numbers in the hbnum.xvg obtained from g_hbond
analysis ??


Data sets 1 and 2.  You will note that there are two columns of data in the 
-hbnum output produced by g_hbond, with titles explaining both.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] problem in running mdrun command

[S.Chandra Shekar]

Dear all

I encounter a problem while running command  mdrun_mpi -v -deffnm em in
gromacs.

I am new to the gromacs. i just ran test calculation, *simulation of
lyzozyme in water*. i am able to generate gro, tpr files. But in the final
step i got following error.

 Thanks in advance.


[localhost.localdomain:23122] mca: base: component_find: paffinity
"mca_paffinity_linux" uses an MCA interface that is not recognized
(component MCA v1.0.0 != supported MCA v2.0.0) -- ignored
[localhost.localdomain:23123] mca: base: component_find: paffinity
"mca_paffinity_linux" uses an MCA interface that is not recognized
(component MCA v1.0.0 != supported MCA v2.0.0) -- ignored
[localhost.localdomain:23123] mca: base: component_find: ras
"mca_ras_dash_host" uses an MCA interface that is not recognized (component
MCA v1.0.0 != supported MCA v2.0.0) -- ignored
[localhost.localdomain:23123] mca: base: component_find: ras
"mca_ras_gridengine" uses an MCA interface that is not recognized
(component MCA v1.0.0 != supported MCA v2.0.0) -- ignored
[localhost.localdomain:23123] mca: base: component_find: ras
"mca_ras_localhost" uses an MCA interface that is not recognized (component
MCA v1.0.0 != supported MCA v2.0.0) -- ignored
[localhost.localdomain:23123] mca: base: component_find: errmgr
"mca_errmgr_hnp" uses an MCA interface that is not recognized (component
MCA v1.0.0 != supported MCA v2.0.0) -- ignored
[localhost.localdomain:23123] mca: base: component_find: errmgr
"mca_errmgr_orted" uses an MCA interface that is not recognized (component
MCA v1.0.0 != supported MCA v2.0.0) -- ignored
[localhost.localdomain:23123] mca: base: component_find: errmgr
"mca_errmgr_proxy" uses an MCA interface that is not recognized (component
MCA v1.0.0 != supported MCA v2.0.0) -- ignored
[localhost.localdomain:23123] mca: base: component_find: iof
"mca_iof_proxy" uses an MCA interface that is not recognized (component MCA
v1.0.0 != supported MCA v2.0.0) -- ignored
[localhost.localdomain:23123] mca: base: component_find: iof "mca_iof_svc"
uses an MCA interface that is not recognized (component MCA v1.0.0 !=
supported MCA v2.0.0) -- ignored
[localhost.localdomain:23122] mca: base: component_find: rcache
"mca_rcache_rb" uses an MCA interface that is not recognized (component MCA
v1.0.0 != supported MCA v2.0.0) -- ignored
[localhost:23122] *** Process received signal ***
[localhost:23122] Signal: Segmentation fault (11)
[localhost:23122] Signal code: Address not mapped (1)
[localhost:23122] Failing at address: 0x4498
[localhost:23122] [ 0] /lib64/libpthread.so.0() [0x3fcee0f500]
[localhost:23122] [ 1] /usr/local/lib/libmpi.so.1(PMPI_Comm_size+0x4e)
[0x2acc6d93727e]
[localhost:23122] [ 2]
/usr/local/gromacs/bin/../lib/libgmx_mpi.so.8(gmx_setup+0x32)
[0x2acc6d195e02]
[localhost:23122] [ 3]
/usr/local/gromacs/bin/../lib/libgmx_mpi.so.8(init_par+0x51)
[0x2acc6d234251]
[localhost:23122] [ 4] mdrun_mpi(cmain+0x11f9) [0x435799]
[localhost:23122] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd)
[0x3fcea1ecdd]
[localhost:23122] [ 6] mdrun_mpi() [0x406ee9]
[localhost:23122] *** End of error message ***
Segmentation fault (core dumped)
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[gmx-users] Re: choosing force field

[pratibha]

Thank you Justin for your kind help. The simple reason for considering only
gromos parameter sets is that the parameters for the metal ions (in my
protein) are not defined in other force fields.


On Sat, Nov 9, 2013 at 7:18 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5012376...@n6.nabble.com> wrote:

>
>
> On 11/9/13 12:48 AM, pratibha wrote:
> > Sorry for the previous mistake. Instead of 53a7, the force field which I
> > used was 53a6.
> >
> >
>
> 53A6 is known to under-stabilize helices, so if a helix did not appear in
> a
> simulation using this force field, it is not definitive proof that the
> structure
> does not populate helical structures.  I generally see mixed opinions in
> the
> literature in terms of which Gromos parameter set is the most reliable.
>  As was
> asked by someone else, is there a reason you are only considering Gromos
> parameter sets?  Others may be better suited to your study.
>
> -Justin
>
> > On Fri, Nov 8, 2013 at 12:10 AM, Justin Lemkul [via GROMACS] <
> > [hidden email] >
> wrote:
> >
> >>
> >>
> >> On 11/7/13 12:14 PM, pratibha wrote:
> >>> My protein contains metal ions which are parameterized only in gromos
> >> force
> >>> field. Since I am a newbie to MD simulations, it would be difficult
> for
> >> me
> >>> to parameterize those myself.
> >>> Can you please guide me as per my previous mail  which out of the two
> >>> simulations should I consider  more reliable-43a1 or 53a7?
> >>
> >> AFAIK, there is no such thing as 53A7, and your original message was
> full
> >> of
> >> similar typos, making it nearly impossible to figure out what you were
> >> actually
> >> doing.  Can you indicate the actual force field(s) that you have been
> >> using in
> >> case someone has any ideas?  The difference between 53A6 and 54A7
> should
> >> be
> >> quite pronounced, in my experience, thus any guesses as to what "53A7"
> >> should be
> >> doing are not productive because I don't know what that is.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 601
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> [hidden email] 
> |
> >> (410) 706-7441
> >>
> >> ==
> >> --
> >> gmx-users mailing list[hidden email]<
> http://user/SendEmail.jtp?type=node&node=5012325&i=1>
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> >> below:
> >>
> >>
>
> >> .
> >> NAML<
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>
> >>
> >
> >
> > --
> > View this message in context:
> http://gromacs.5086.x6.nabble.com/choosing-force-field-tp5012242p5012370.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> [hidden email]  |
> (410) 706-7441
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[gmx-users] Umbrella Sampling tutorial

[shahab shariati]

Dear Justin

Thanks for your reply.

You are right. I should  not extrapolate too literally from your tutorial
to my system.

But, I have a general question:

There is 2 groups in COM pulling method (reference group + pull group).

If I want to use pull_geometry = distance, so, I should fix reference group
to be immobile. Is it true?

On the other hand, I want to know exactly using position restraining on
reference group is optional or mandatory in COM pulling method?

Best wishes
-- 
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Re: mdrun on 8-core AMD + GTX TITAN (was: Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs)

[Mark Abraham]

On Sun, Nov 10, 2013 at 5:28 AM, Dwey Kauffman  wrote:

> Hi Szilard,
>
>  Thank you very much for your suggestions.
>
> >Actually, I was jumping to conclusions too early, as you mentioned AMD
> >"cluster", I assumed you must have 12-16-core Opteron CPUs. If you
> >have an 8-core (desktop?) AMD CPU, than you may not need to run more
> >than one rank per GPU.
>
> Yes, we do have independent clusters of AMD, AMD opteron, Intel Corei7. All
> nodes of three clusters are  installed with (at least) 1 GPU card.   I have
> run the same test on these three clusters.
>
> Let's focus on a basic scaling issue:  One GPU  v.s Two GPUs within the
> same
> node of 8-core AMD cpu.
> Using 1 GPU, we  can  have a performance of ~32 ns/day.  Using two GPU, we
> gain not much more ( ~38.5 ns/day ).  It is about ~20% more performance.
> However, this is not really true because in some tests, I also saw only
> 2-5%
> more, which really surprised me.


Neither run had a PP-PME work distribution suitable for the hardware it was
running on (and fixing that for each run requires opposite changes). Adding
a GPU and hoping to see scaling requires that there be proportionately more
GPU work available to do, *and* enough absolute work to do. mdrun tries to
do this, and reports early in the log file, which is one of the reasons
Szilard asked to see whole log files - please use a file sharing service to
do that.

As you can see, this test was made on the same node regardless of
> networking.  Can the performance be improved  say 50% more when 2 GPUs are
> used on a general task ?  If yes, how ?
>
> >Indeed, as Richard pointed out, I was asking for *full* logs, these
> >summaries can't tell much, the table above the summary entitled "R E A
> >L   C Y C L E   A N D   T I M E   A C C O U N T I N G" as well as
> >other reported information across the log file is what I need to make
> >an assessment of your simulations' performance.
>
> Please see below.
>
> >>However, in your case I suspect that the
> >>bottleneck is multi-threaded scaling on the AMD CPUs and you should
> >>probably decrease the number of threads per MPI rank and share GPUs
> >>between 2-4 ranks.
>
> After I test all three clusters, I found it may NOT be an issue of AMD
> cpus.
> Intel cpus has the SAME scaling issue.
>
> However, I am curious as to how you justify the setup of 2-4 ranks sharing
> GPUs ? Can you please explain it a bit more ?
>

NUMA effects on multi-socket AMD processors are particularly severe; the
way GROMACS uses OpenMP is not well suited to them. Using a rank (or two)
per socket will greatly reduce those effects, but introduces different
algorithmic overhead from the need to do DD and explicitly communicate
between ranks. (You can see the latter in your .log file snippets below.)
Also, that means the parcel of PP work available from a rank to give to the
GPU is smaller, which is the opposite of what you'd like for GPU
performance and/or scaling. We are working on a general solution for this
and lots of related issues in the post-5.0 space, but there is a very hard
limitation imposed by the need to amortize the cost of CPU-GPU transfer by
having lots of PP work available to do.

>You could try running
> >mpirun -np 4 mdrun -ntomp 2 -gpu_id 0011
> >but I suspect this won't help because your scaling issue
>
> Your guess is correct but why is that ?  it is worse. The more nodes are
> involved in a task, the performance is worse.
>
>
> >> in my
> >>experience even reaction field runs don't scale across nodes with 10G
> >>ethernet if you have more than 4-6 ranks per node trying to
> >>communicate (let alone with PME).
>
> What dose it mean " let alone with PME" ?  how to do so ? by mdrun ?
> I do know " mdrun -npme to specify PME process.
>

If using PME (rather than RF), network demands are more severe.


> Thank you.
>
> Dwey
>
>
>
> ### One GPU 
>
>  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>
>  Computing: Nodes   Th. Count  Wall t (s) G-Cycles   %
>
> -
>  Neighbor search18 11 431.81713863.390 1.6
>  Launch GPU ops.18501 472.90615182.556 1.7
>  Force  185011328.61142654.785 4.9
>  PME mesh   18501   11561.327   371174.09042.8
>  Wait GPU local 185016888.008   221138.11125.5
>  NB X/F buffer ops. 189911216.49939055.455 4.5
>  Write traj.18   1030  12.741  409.039 0.0
>  Update 185011696.35854461.226 6.3
>  Constraints185011969.72663237.647 7.3
>  Rest   11458.82046835.133 5.4
>
> -
>  Total  1   2

Re: [gmx-users] About Compiler Compatibility for Gromacs 4.6.2 Compilation

[Mark Abraham]

On Nov 10, 2013 10:04 AM, "Mark Abraham"  wrote:

> Yes (unless you are using AMD cpus), per the installation instructions,
> although you will probably do slightly better with GCC 4.7, and should not
> do a new install of 4.6.2 after 4.6.3 is released. In particular, 4.6.2 has
> an affinity-related performance regression when using external MPI
> libraries.
>
> Mark
> On Nov 10, 2013 7:55 AM, "vidhya sankar"  wrote:
>
>>
>>
>> Dear Justin and Mark Thank you for your Previous reply
>> Can i Use the Following Intel  Compiler  for grmacs 4.6.2
>> in centos Linux OS ?
>>
>>  Intel® C++ Composer XE 2013 for Linux
>>
>> it Includes Intel® C++ Compiler, Intel® Integrated Performance Primitives
>> 7.1, Intel® Math Kernel Library 11.0,
>> Intel Cilk™ Plus, the Intel® Threading Building Blocks (Intel® TBB)”
>>
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