subject:"\[gmx\-users\] Re\:"




On 11/11/13 12:08 PM, Williams Ernesto Miranda Delgado wrote:

Hello
If I did the MD simulation using PME and neutralized with ions, and I want
to rerun this time with reaction field zero, is there any problem if I
keep the ions? This is for LIE calculation. I am using AMBER99SB.


Why do you think it necessary to delete them?

-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: Reaction field zero and ions

2013-11-12 Thread Dr. Vitaly Chaban

There are no problems to have ions while using Reaction-Field treatment.


Dr. Vitaly V. Chaban


On Mon, Nov 11, 2013 at 7:06 PM, Justin Lemkul jalem...@vt.edu wrote:


 On 11/11/13 12:08 PM, Williams Ernesto Miranda Delgado wrote:

 Hello
 If I did the MD simulation using PME and neutralized with ions, and I want
 to rerun this time with reaction field zero, is there any problem if I
 keep the ions? This is for LIE calculation. I am using AMBER99SB.


 Why do you think it necessary to delete them?

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




On 11/11/13 5:39 PM, bharat gupta wrote:

Sorry, I attached the wrong file . Here's the average file generate from
one of the files I sent in my last mail. I used the command g_analyze -f
hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained
from this command :-

https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg

Now, if you see, the graph (in previous mail) and average file, both
correlates well. I have a doubt about interpreting the result from
g_analyze. The value 7.150740e+00 implies that on average 7 hydrogen
bonds are formed during the simulation time of 5ns to 10ns. What does then
the average file or its graph tells ??



It's an average over sets.  It is not equivalent to the output printed to the 
screen, nor is it supposed to.  The value printed to the screen is the actual 
average of the data set of interest, as is intuitive from your values.  An 
average of 4 is impossible if all the data points are in the range of 6-9.


-Justin




On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul jalem...@vt.edu wrote:




On 11/11/13 4:06 AM, bharat gupta wrote:


In addition to my previous question, I have another question about
g_analyze. When I used the hbond.xvg file to get the average and plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its final calculation gives 7.150
as the average values... Here's the link for the graph and result of
average value calculated by g_analyze :-

std. dev.relative deviation of
 standard   -   cumulants from those of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
cum. 3   cum. 4
SS1  * 7.150740e+00 *  8.803173e-01   1.760635e-02   0.0620.163

SS2   1.490604e+00   1.164761e+00   2.329523e-02   0.4950.153

https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png

Here's the  link hbond.xvg file and its averaged file
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg



Neither of these files produce output that corresponds to the PNG image
above. Both files have values in 6-9 H-bond range and thus agree with the
g_analyze output, which I can reproduce.  I suspect you're somehow getting
your files mixed up.


-Justin



On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta bharat.85.m...@gmail.com
wrote:

  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 jalem...@vt.edu 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 jalem...@vt.edu

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


  --

==

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
* Please search the archive at

Re: [gmx-users] Re: g_analyze




On 11/11/13 6:56 PM, bharat gupta wrote:

Hi,

I tried g_select to dump the structure with the interacting water
molecules, but I don't know know how to do that. I searched for some
threads in the discussion but wasn't able to find anything related to my
need. Can you explain how can I do that ?



Start with g_select -select 'help all' and see what you can determine.  Such 
selections are rather straightforward and have been explained several times on 
the list.  If you need help, show us what you're doing and describe why it isn't 
what you want.  It will ultimately save a lot of time.


-Justin



On Tue, Nov 12, 2013 at 7:39 AM, bharat gupta bharat.85.m...@gmail.comwrote:


Sorry, I attached the wrong file . Here's the average file generate from
one of the files I sent in my last mail. I used the command g_analyze -f
hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained
from this command :-

https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg

Now, if you see, the graph (in previous mail) and average file, both
correlates well. I have a doubt about interpreting the result from
g_analyze. The value 7.150740e+00 implies that on average 7 hydrogen
bonds are formed during the simulation time of 5ns to 10ns. What does then
the average file or its graph tells ??



On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul jalem...@vt.edu wrote:




On 11/11/13 4:06 AM, bharat gupta wrote:


In addition to my previous question, I have another question about
g_analyze. When I used the hbond.xvg file to get the average and plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its final calculation gives
7.150
as the average values... Here's the link for the graph and result of
average value calculated by g_analyze :-

std. dev.relative deviation of
 standard   -   cumulants from those
of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
cum. 3   cum. 4
SS1  * 7.150740e+00 *  8.803173e-01   1.760635e-02   0.0620.163

SS2   1.490604e+00   1.164761e+00   2.329523e-02   0.4950.153

https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png

Here's the  link hbond.xvg file and its averaged file
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg



Neither of these files produce output that corresponds to the PNG image
above. Both files have values in 6-9 H-bond range and thus agree with the
g_analyze output, which I can reproduce.  I suspect you're somehow getting
your files mixed up.


-Justin



On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta bharat.85.m...@gmail.com
wrote:

  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 jalem...@vt.edu
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 jalem...@vt.edu

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


  --

==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room

Re: [gmx-users] Re: g_analyze

2013-11-12 Thread bharat gupta

Thanks justin for your replies. I understood the g_analyze related data. I
tired g_analyze to dump the structures as you said. But, I didn't find any
switch that can be used to dump the structure in pdb format.


On Tue, Nov 12, 2013 at 10:15 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/11/13 6:56 PM, bharat gupta wrote:

 Hi,

 I tried g_select to dump the structure with the interacting water
 molecules, but I don't know know how to do that. I searched for some
 threads in the discussion but wasn't able to find anything related to my
 need. Can you explain how can I do that ?


 Start with g_select -select 'help all' and see what you can determine.
  Such selections are rather straightforward and have been explained several
 times on the list.  If you need help, show us what you're doing and
 describe why it isn't what you want.  It will ultimately save a lot of time.

 -Justin



 On Tue, Nov 12, 2013 at 7:39 AM, bharat gupta bharat.85.m...@gmail.com
 wrote:

  Sorry, I attached the wrong file . Here's the average file generate from
 one of the files I sent in my last mail. I used the command g_analyze -f
 hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained
 from this command :-

 https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg

 Now, if you see, the graph (in previous mail) and average file, both
 correlates well. I have a doubt about interpreting the result from
 g_analyze. The value 7.150740e+00 implies that on average 7 hydrogen
 bonds are formed during the simulation time of 5ns to 10ns. What does
 then
 the average file or its graph tells ??



 On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/11/13 4:06 AM, bharat gupta wrote:

  In addition to my previous question, I have another question about
 g_analyze. When I used the hbond.xvg file to get the average and
 plotted
 the average.xvg file I found that the average value is round 4 to 5
 according to the graph. But g_analyze in its final calculation gives
 7.150
 as the average values... Here's the link for the graph and result of
 average value calculated by g_analyze :-

 std. dev.relative deviation of
  standard   -   cumulants from
 those
 of
 set  average   deviation  sqrt(n-1)   a Gaussian
 distribition
 cum. 3   cum. 4
 SS1  * 7.150740e+00 *  8.803173e-01   1.760635e-02   0.0620.163

 SS2   1.490604e+00   1.164761e+00   2.329523e-02   0.4950.153

 https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png

 Here's the  link hbond.xvg file and its averaged file
 https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
 https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg


  Neither of these files produce output that corresponds to the PNG
 image
 above. Both files have values in 6-9 H-bond range and thus agree with
 the
 g_analyze output, which I can reproduce.  I suspect you're somehow
 getting
 your files mixed up.


 -Justin


  On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta 
 bharat.85.m...@gmail.com
 wrote:

   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 jalem...@vt.edu
 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 jalem...@vt.edu

 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
 * Please search the archive at http://www.gromacs.org/
 Support/Mailing_Lists/Search before

Re: [gmx-users] Re: g_analyze




On 11/12/13 8:33 AM, bharat gupta wrote:

Thanks justin for your replies. I understood the g_analyze related data. I
tired g_analyze to dump the structures as you said. But, I didn't find any
switch that can be used to dump the structure in pdb format.



Because that's not the function of g_analyze.  Use trjconv -dump with a suitable 
index file (from g_select).


-Justin



On Tue, Nov 12, 2013 at 10:15 PM, Justin Lemkul jalem...@vt.edu wrote:




On 11/11/13 6:56 PM, bharat gupta wrote:


Hi,

I tried g_select to dump the structure with the interacting water
molecules, but I don't know know how to do that. I searched for some
threads in the discussion but wasn't able to find anything related to my
need. Can you explain how can I do that ?



Start with g_select -select 'help all' and see what you can determine.
  Such selections are rather straightforward and have been explained several
times on the list.  If you need help, show us what you're doing and
describe why it isn't what you want.  It will ultimately save a lot of time.

-Justin




On Tue, Nov 12, 2013 at 7:39 AM, bharat gupta bharat.85.m...@gmail.com
wrote:

  Sorry, I attached the wrong file . Here's the average file generate from

one of the files I sent in my last mail. I used the command g_analyze -f
hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained
from this command :-

https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg

Now, if you see, the graph (in previous mail) and average file, both
correlates well. I have a doubt about interpreting the result from
g_analyze. The value 7.150740e+00 implies that on average 7 hydrogen
bonds are formed during the simulation time of 5ns to 10ns. What does
then
the average file or its graph tells ??



On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul jalem...@vt.edu wrote:




On 11/11/13 4:06 AM, bharat gupta wrote:

  In addition to my previous question, I have another question about

g_analyze. When I used the hbond.xvg file to get the average and
plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its final calculation gives
7.150
as the average values... Here's the link for the graph and result of
average value calculated by g_analyze :-

 std. dev.relative deviation of
  standard   -   cumulants from
those
of
set  average   deviation  sqrt(n-1)   a Gaussian
distribition
 cum. 3   cum. 4
SS1  * 7.150740e+00 *  8.803173e-01   1.760635e-02   0.0620.163

SS2   1.490604e+00   1.164761e+00   2.329523e-02   0.4950.153

https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png

Here's the  link hbond.xvg file and its averaged file
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg


  Neither of these files produce output that corresponds to the PNG

image
above. Both files have values in 6-9 H-bond range and thus agree with
the
g_analyze output, which I can reproduce.  I suspect you're somehow
getting
your files mixed up.


-Justin


  On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta 

bharat.85.m...@gmail.com
wrote:

   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 jalem...@vt.edu
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 jalem...@vt.edu


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
*

[gmx-users] Re: ok, thank you

2013-11-12 Thread Williams Ernesto Miranda Delgado

 Send gmx-users mailing list submissions to
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 than Re: Contents of gmx-users digest...


 Today's Topics:

1. Restarting a simulation after replacing an empty md.trr file
   (arun kumar)
2. Re: Re: Reaction field zero and ions (Justin Lemkul)
3. Re: Calculating diffusion coefficient in three dimension
   (Dr. Vitaly Chaban)
4. Re: Re: Reaction field zero and ions (Dr. Vitaly Chaban)
5. Re: Re: g_analyze (Justin Lemkul)
6. Re: Re: g_analyze (Justin Lemkul)


 --

 Message: 1
 Date: Tue, 12 Nov 2013 11:45:05 +0530
 From: arun kumar arunjones.kuma...@gmail.com
 Subject: [gmx-users] Restarting a simulation after replacing an empty
   md.trr  file
 To: gmx-users@gromacs.org
 Message-ID:
   cagm9vj8dn+fqb-cigjdvv+i1mq7mc2cxvkde3gsp5+lwhds...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 Dear Gromacs users,

 I am running a 50ns simulation of a protein having nearly 700 residues on
 60 threads (Gromacs 4.6.3).
 At one point i got a disk space problem, so i have deleted the md.trr file
 and created an empty md.trr file. when i tried to restart the simulation
 from check point file on 100 threads, [ mdrun -v -deffnm md -cpi md.cpt
 -nt
 100 ]
 i am getting a note and an error as fallows

 Reading checkpoint file md.cpt generated:
   #PME-nodes mismatch,
 current program: 100
 checkpoint file: 60
 Gromacs binary or parallel settings not identical to previous run.
 Continuation is exact, but is not guaranteed to be binary identical.
 ...

 Source code file: checkpoint.c, line: 1767
 Fatal error:
 Can't read 1048576 bytes of 'md.trr' to compute checksum. The file
 has been replaced or its contents has been modified.

 please help me in overcoming this problem.

 Thanking you.

 --
 Arun Kumar Somavarapu
 Project-JRF
 Dr. Pawan Gupta's lab
 Protein Science and Engineering Dept,
 Institute of Microbial Tecnology,
 Sec 39-A, Chandigarh - 160036.


 --

 Message: 2
 Date: Mon, 11 Nov 2013 13:06:32 -0500
 From: Justin Lemkul jalem...@vt.edu
 Subject: Re: [gmx-users] Re: Reaction field zero and ions
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID: 52811ca8.5030...@vt.edu
 Content-Type: text/plain; charset=ISO-8859-1; format=flowed



 On 11/11/13 12:08 PM, Williams Ernesto Miranda Delgado wrote:
 Hello
 If I did the MD simulation using PME and neutralized with ions, and I
 want
 to rerun this time with reaction field zero, is there any problem if I
 keep the ions? This is for LIE calculation. I am using AMBER99SB.

 Why do you think it necessary to delete them?

 -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

 ==


 --

 Message: 3
 Date: Tue, 12 Nov 2013 13:02:54 +0100
 From: Dr. Vitaly Chaban vvcha...@gmail.com
 Subject: Re: [gmx-users] Calculating diffusion coefficient in three
   dimension
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID:
   capxdd+abay6mj_dkn6_k+mkbuty4eyzspdvdxj+m-m-2zae...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 MSD is 3D by default.


 Dr. Vitaly V. Chaban


 On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote:
 Dear all,
 I am simulating a spherical lipid vesicle. I want to calculate the
 diffusion coefficient for each lipid component in 3D. How to calculate
 it
 using g_msd (or any other tool like g_velacc)?

 Thank you for your concern

 --
 With Best Wishes
 Venkat Reddy Chirasani
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 Message: 4
 Date: Tue, 12 Nov 2013 13:04:10 +0100
 From: Dr. Vitaly Chaban vvcha...@gmail.com
 Subject: Re: [gmx-users] Re: Reaction field zero and ions
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID:
   capxdd+zuwgcfdx+hymrgi7tm4pa5fnczemr+tdswd5yqvaq

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

2013-11-12 Thread Szilárd Páll

501 358.1200.072 1.8
 -
  Total  20029.8464.006   100.0
 -

 Force evaluation time GPU/CPU: 4.006 ms/2.578 ms = 1.554
 For optimal performance this ratio should be close to 1!


 NOTE: The GPU has 20% more load than the CPU. This imbalance causes
   performance loss, consider using a shorter cut-off and a finer PME
 grid.

Core t (s)   Wall t (s)(%)
Time:   216205.51027036.812  799.7
  7h30:36
  (ns/day)(hour/ns)
 Performance:   31.9560.751


 ### Two GPUs #

  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   %
 -
  Domain decomp. 24 10 339.49010900.191 1.5
  DD comm. load  24  49989   0.2628.410 0.0
  Neighbor search24 11 481.58315462.464 2.2
  Launch GPU ops.24   1002 579.28318599.358 2.6
  Comm. coord.   24490 523.09616795.351 2.3
  Force  245011545.58449624.951 6.9
  Wait + Comm. F 24501 821.74026384.083 3.7
  PME mesh   24501   11097.880   356326.03049.5
  Wait GPU nonlocal  245011001.86832167.550 4.5
  Wait GPU local 24501   8.613  276.533 0.0
  NB X/F buffer ops. 24   19821061.23834073.781 4.7
  Write traj.24   1025   5.681  182.419 0.0
  Update 245011692.23354333.503 7.6
  Constraints245012316.14574365.78810.3
  Comm. energies 24101  15.802  507.373 0.1
  Rest   2 908.38329165.963 4.1
 -
  Total  2   22398.880   719173.747   100.0
 -
 -
  PME redist. X/F24   10021519.28848780.654 6.8
  PME spread/gather  24   10025398.693   173338.93624.1
  PME 3D-FFT 24   10022798.48289852.48212.5
  PME 3D-FFT Comm.   24   1002 947.03330406.937 4.2
  PME solve  24501 420.66713506.611 1.9
 -

Core t (s)   Wall t (s)(%)
Time:   178961.45022398.880  799.0
  6h13:18
  (ns/day)(hour/ns)
 Performance:   38.5730.622






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[gmx-users] Re: segmentation fault on gromacs 4.5.5 after mdrun

2013-11-12 Thread cjalmeciga

I run

grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

and everything looks fine. I check the nvt.tpr, and temperature is ok.

the real problem is with the mdrun function.

could be a problem of the software?

Thanks

Javier

Justin Lemkul wrote
On 11/11/13 11:24 AM, Carlos Javier Almeciga Diaz wrote:
Hello evryone,

I doing a simulation of a ligand-protein interaction with gromacs 4.5.5.
Everything looks fine after I equilibrate the protein-ligand complex. I'm
running these commands:

grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

mdrun -deffnm nvt

Nevertheless, I got this error:

Reading file nvt.tpr, VERSION 4.5.5 (double precision)
Segmentation fault

What should I do?

Instantaneous failure typically indicates that the forces are
nonsensically high
and the constraint algorithm immediately fails. Likely the previous
energy
minimization did not adequately complete.

-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

jalemkul@.umaryland

| (410) 706-7441

==
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[gmx-users] Re: Restarting a simulation after replacing an empty md.trr file

2013-11-12 Thread arunjones

Hello Sir,
Thanks for the reply.
now is it fine if i use 100 threads in my restart.
is there any impact on the over all simulation? 

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Re: [gmx-users] Re: segmentation fault on gromacs 4.5.5 after mdrun

On 11/12/13 10:58 AM, cjalmeciga wrote:

I run

grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

and everything looks fine. I check the nvt.tpr, and temperature is ok.

The fact that grompp completes indicates there is nothing syntactically wrong
with the input files. Whether or not the content of the .mdp is physically
sensible or the input configuration is plausible is an entirely different
matter. Please tell us what the exact outcome of the previous energy
minimization was (potential energy, maximum force, copied and pasted from screen
output or .log file).

the real problem is with the mdrun function.

could be a problem of the software?

You have presented no evidence that would lead anyone to believe the problem is
with mdrun. In the vast majority of cases, user input is the problem.

-Justin

Thanks

Javier

Justin Lemkul wrote

On 11/11/13 11:24 AM, Carlos Javier Almeciga Diaz wrote:

Hello evryone,

I doing a simulation of a ligand-protein interaction with gromacs 4.5.5.
Everything looks fine after I equilibrate the protein-ligand complex. I'm
running these commands:

grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

mdrun -deffnm nvt

Nevertheless, I got this error:

Reading file nvt.tpr, VERSION 4.5.5 (double precision)
Segmentation fault

What should I do?

Instantaneous failure typically indicates that the forces are
nonsensically high
and the constraint algorithm immediately fails. Likely the previous
energy
minimization did not adequately complete.

-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

jalemkul@.umaryland

| (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: Restarting a simulation after replacing an empty md.trr file




On 11/12/13 11:10 AM, arunjones wrote:

Hello Sir,
Thanks for the reply.
now is it fine if i use 100 threads in my restart.
is there any impact on the over all simulation?



Only if that is the number of threads originally used in the run.  If not, there 
will be a mismatch between the DD grid setup, the .cpt file will complain, and 
the run will fail.  Rule of thumb: don't change settings or alter files mid-run ;)


-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: Restarting a simulation after replacing an empty md.trr file

2013-11-12 Thread arunjones

Thank you Sir,
initially i was running on 60 threads, now i changed it to 100. simulation
is running with out any error, but i found a note in the log file as fallows

  #nodes mismatch,
current program: 100
checkpoint file: 60

  #PME-nodes mismatch,
current program: -1
checkpoint file: 12

Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical.

Initializing Domain Decomposition on 100 nodes


is it a good idea to continue or shall i stick with 60 threads.

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Re: [gmx-users] Re: Restarting a simulation after replacing an empty md.trr file




On 11/12/13 12:07 PM, arunjones wrote:

Thank you Sir,
initially i was running on 60 threads, now i changed it to 100. simulation
is running with out any error, but i found a note in the log file as fallows

   #nodes mismatch,
 current program: 100
 checkpoint file: 60

   #PME-nodes mismatch,
 current program: -1
 checkpoint file: 12

Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical.

Initializing Domain Decomposition on 100 nodes


is it a good idea to continue or shall i stick with 60 threads.



Like I said, I think it is a bad idea to switch settings haphazardly during the 
run.  As the note indicates, the continuation is exact, but not binary 
identical.  Check the website for what all that means if you're not sure.


-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: segmentation fault on gromacs 4.5.5 after mdrun

2013-11-12 Thread cjalmeciga

The output of energy minimization was

Potential Energy = -1.42173622068236e+06
Maximum force = 9.00312066109319e+02 on atom 148
Norm of force = 2.06087515037187e+01

Thanks

Javier

Justin Lemkul wrote
On 11/12/13 10:58 AM, cjalmeciga wrote:
I run

grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

and everything looks fine. I check the nvt.tpr, and temperature is ok.

The fact that grompp completes indicates there is nothing syntactically
wrong
with the input files. Whether or not the content of the .mdp is
physically
sensible or the input configuration is plausible is an entirely different
matter. Please tell us what the exact outcome of the previous energy
minimization was (potential energy, maximum force, copied and pasted from
screen
output or .log file).

the real problem is with the mdrun function.

could be a problem of the software?

You have presented no evidence that would lead anyone to believe the
problem is
with mdrun. In the vast majority of cases, user input is the problem.

-Justin

Thanks

Javier

Justin Lemkul wrote
On 11/11/13 11:24 AM, Carlos Javier Almeciga Diaz wrote:
Hello evryone,

I doing a simulation of a ligand-protein interaction with gromacs
4.5.5.
Everything looks fine after I equilibrate the protein-ligand complex.
I'm
running these commands:

grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

mdrun -deffnm nvt

Nevertheless, I got this error:

Reading file nvt.tpr, VERSION 4.5.5 (double precision)
Segmentation fault

What should I do?

Instantaneous failure typically indicates that the forces are
nonsensically high
and the constraint algorithm immediately fails. Likely the previous
energy
minimization did not adequately complete.

-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

jalemkul@.umaryland

| (410) 706-7441

==
--
gmx-users mailing list

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gmx-users-request@

.
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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

jalemkul@.umaryland

| (410) 706-7441

==
--
gmx-users mailing list

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Re: [gmx-users] Re: segmentation fault on gromacs 4.5.5 after mdrun

On 11/12/13 12:14 PM, cjalmeciga wrote:

The output of energy minimization was

Potential Energy = -1.42173622068236e+06
Maximum force = 9.00312066109319e+02 on atom 148
Norm of force = 2.06087515037187e+01

OK, reasonable enough. How about a description of what the system is, which
force field you chose, how you derived the ligand topology, and the full
contents of your .mdp file?

-Justin

Thanks

Javier

Justin Lemkul wrote

On 11/12/13 10:58 AM, cjalmeciga wrote:

I run

grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

and everything looks fine. I check the nvt.tpr, and temperature is ok.

The fact that grompp completes indicates there is nothing syntactically
wrong
with the input files. Whether or not the content of the .mdp is
physically
sensible or the input configuration is plausible is an entirely different
matter. Please tell us what the exact outcome of the previous energy
minimization was (potential energy, maximum force, copied and pasted from
screen
output or .log file).

the real problem is with the mdrun function.

could be a problem of the software?

You have presented no evidence that would lead anyone to believe the
problem is
with mdrun. In the vast majority of cases, user input is the problem.

-Justin

Thanks

Javier

Justin Lemkul wrote

On 11/11/13 11:24 AM, Carlos Javier Almeciga Diaz wrote:

Hello evryone,

I doing a simulation of a ligand-protein interaction with gromacs
4.5.5.
Everything looks fine after I equilibrate the protein-ligand complex.
I'm
running these commands:

grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

mdrun -deffnm nvt

Nevertheless, I got this error:

Reading file nvt.tpr, VERSION 4.5.5 (double precision)
Segmentation fault

What should I do?

Instantaneous failure typically indicates that the forces are
nonsensically high
and the constraint algorithm immediately fails. Likely the previous
energy
minimization did not adequately complete.

-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

jalemkul@.umaryland

| (410) 706-7441

==
--
gmx-users mailing list

gmx-users@

gmx-users-request@

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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

jalemkul@.umaryland

| (410) 706-7441

==
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gmx-users-request@

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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

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

[gmx-users] Re: Change in the position of structural Zinc and calcium ions during MD

2013-11-12 Thread Rama

Hi Justin,

Below I pasted .mdp file and topology. In .log file I could see energy term
for position restraints.

.mdp file---
title   = NPT Equilibration 
define  = -DPOSRES  ; position restraints for protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 50; 2 * 50 = 1000 ps (1 ns)
dt  = 0.002 ; 2 fs
; Output control
nstxout = 500   ; save coordinates every 1 ps
nstvout = 500   ; save velocities every 1 ps
nstenergy   = 500   ; save energies every 1 ps
nstlog  = 500   ; update log file every 1 ps
; Bond parameters
continuation= yes   ; Restarting after NVT 
constraint_algorithm = lincs; holonomic constraints 
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = Nose-Hoover   ; More accurate thermostat
tc-grps =  Protein_CA_ZN   DMPC   SOL_CL; three coupling groups 
- more
accurate
tau_t   =   0.50.5 0.5  ; time constant, in ps
ref_t   =   298298 310  ; reference 
temperature, one for
each group, in K
; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype  = semiisotropic ; uniform scaling of x-y box 
vectors,
independent z
tau_p   = 5.0   ; time constant, in ps
ref_p   = 1.0   1.0 ; reference pressure, x-y, z 
(in bar)
compressibility = 4.5e-54.5e-5  ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode   = Linear
comm-grps   = Protein_DMPC SOL_CL
; Scale COM of reference coordinates
refcoord_scaling = com


topol.top
; Include Position restraint file
#ifdef POSRES
#include posre.itp
#endif

; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#include strong_posre.itp
#endif

; Include DMPC topology
 #include rama4LJ.ff/dmpcLJ.itp

; Include water topology
#include rama4LJ.ff/spc.itp

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include rama4LJ.ff/ions.itp

---.log file
   Energies (kJ/mol)
  AngleProper Dih. Ryckaert-Bell.  Improper Dih.  LJ-14
1.77761e+043.10548e+037.97673e+034.40586e+028.14131e+03
 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
2.59758e+042.74092e+04   -2.56846e+03   -4.68637e+05   -1.67418e+05
 Position Rest.  PotentialKinetic En.   Total EnergyTemperature
7.09403e+02   -5.47088e+058.83115e+04   -4.58777e+053.07118e+02
 Pres. DC (bar) Pressure (bar)   Constr. rmsd
   -2.00493e+021.00080e+000.0e+00


Thanks

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

2013-11-12 Thread Dwey Kauffman

more hardware at it. To hope to see some
scaling, you'd need to be able to drop the PME mesh time by about a factor
of two (coarser grid, and compensating increase to rcoulomb), and hope
there was enough PP work that using two GPUs for a single simulation is
even worth considering. Achieving throughput-style scaling by running two
independent simulations on the same node may be all that is practical (but
I don't even know how many atoms you are simulating!)

Mark
In the configuration of two GPUs, there is NO such GPU timing table, while
in that of 1 GPU there is one. See logs.

Again, it is interesting to know if there was enough PP work for two GPUs.
Increasing cuf-offs indeed achieves this purpose when cutoff 1.6 but the
total performance (ns/day) decreases severely. That's NOT what I want
because I would like to assign 0.8 or 1.0 or 1.2 nm to cutoffs for general
purposes. In this tested case, I am testing Justin's umbrella's pull-code
in his tutorial.

I should also mention that using two GPUs with INTEL 12-core CPUs, I work
on a protein with 35,000 atoms including solvent and ions for general
purposes. Its performance only increases 5-8% more with 2 GPUs.

Beside your hint of PP workload, any better suggestions in practice are
highly appreciated. I can test your suggestion.

Thanks,
Dewey

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Re: [gmx-users] Re: Change in the position of structural Zinc and calcium ions during MD




On 11/12/13 1:47 PM, Rama wrote:

Hi Justin,

Below I pasted .mdp file and topology. In .log file I could see energy term
for position restraints.

.mdp file---
title   = NPT Equilibration
define  = -DPOSRES  ; position restraints for protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 50; 2 * 50 = 1000 ps (1 ns)
dt  = 0.002 ; 2 fs
; Output control
nstxout = 500   ; save coordinates every 1 ps
nstvout = 500   ; save velocities every 1 ps
nstenergy   = 500   ; save energies every 1 ps
nstlog  = 500   ; update log file every 1 ps
; Bond parameters
continuation= yes   ; Restarting after NVT
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = Nose-Hoover   ; More accurate thermostat
tc-grps =  Protein_CA_ZN   DMPC   SOL_CL; three coupling groups 
- more
accurate
tau_t   =   0.50.5 0.5  ; time constant, in ps
ref_t   =   298298 310  ; reference 
temperature, one for
each group, in K
; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype  = semiisotropic ; uniform scaling of x-y box 
vectors,
independent z
tau_p   = 5.0   ; time constant, in ps
ref_p   = 1.0   1.0 ; reference pressure, x-y, z 
(in bar)
compressibility = 4.5e-54.5e-5  ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode   = Linear
comm-grps   = Protein_DMPC SOL_CL
; Scale COM of reference coordinates
refcoord_scaling = com


topol.top
; Include Position restraint file
#ifdef POSRES
#include posre.itp
#endif

; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#include strong_posre.itp
#endif

; Include DMPC topology
  #include rama4LJ.ff/dmpcLJ.itp

; Include water topology
#include rama4LJ.ff/spc.itp

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
11   1000   1000   1000
#endif

; Include topology for ions
#include rama4LJ.ff/ions.itp



Do you have appropriate [position_restraints] assigned in this topology?  None 
of the above, as shown, pertains to the ions, and the only relevant #ifdef block 
that would be triggered by -DPOSRES is for the protein.


-Justin


---.log file
Energies (kJ/mol)
   AngleProper Dih. Ryckaert-Bell.  Improper Dih.  LJ-14
 1.77761e+043.10548e+037.97673e+034.40586e+028.14131e+03
  Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
 2.59758e+042.74092e+04   -2.56846e+03   -4.68637e+05   -1.67418e+05
  Position Rest.  PotentialKinetic En.   Total EnergyTemperature
 7.09403e+02   -5.47088e+058.83115e+04   -4.58777e+053.07118e+02
  Pres. DC (bar) Pressure (bar)   Constr. rmsd
-2.00493e+021.00080e+000.0e+00


Thanks

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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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gmx-users mailing

[gmx-users] Re: Bilayer COM removal issue: Large VCM

2013-11-12 Thread rajat desikan

Hi All,
Any suggestions?

Thanks,


On Mon, Nov 11, 2013 at 12:38 AM, rajat desikan rajatdesi...@gmail.comwrote:

 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
 248.00.0 Large 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+05 LJ (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+29 Large 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+29
 Large 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+29 Large 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




-- 
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] Re: g_analyze

2013-11-11 Thread bharat gupta

In addition to my previous question, I have another question about
g_analyze. When I used the hbond.xvg file to get the average and plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its final calculation gives 7.150
as the average values... Here's the link for the graph and result of
average value calculated by g_analyze :-

  std. dev.relative deviation of
   standard   -   cumulants from those of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
  cum. 3   cum. 4
SS1  * 7.150740e+00 *  8.803173e-01   1.760635e-02   0.0620.163
SS2   1.490604e+00   1.164761e+00   2.329523e-02   0.4950.153

https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png

Here's the  link hbond.xvg file and its averaged file
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg


On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta bharat.85.m...@gmail.comwrote:

 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 jalem...@vt.edu 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 jalem...@vt.edu 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

2013-11-11 Thread Justin Lemkul




On 11/11/13 1:30 AM, bharat gupta wrote:

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 ??



g_select

-Justin



On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul jalem...@vt.edu 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 jalem...@vt.edu 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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==

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

2013-11-11 Thread Justin Lemkul




On 11/11/13 4:06 AM, bharat gupta wrote:

In addition to my previous question, I have another question about
g_analyze. When I used the hbond.xvg file to get the average and plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its final calculation gives 7.150
as the average values... Here's the link for the graph and result of
average value calculated by g_analyze :-

   std. dev.relative deviation of
standard   -   cumulants from those of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
   cum. 3   cum. 4
SS1  * 7.150740e+00 *  8.803173e-01   1.760635e-02   0.0620.163
SS2   1.490604e+00   1.164761e+00   2.329523e-02   0.4950.153

https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png

Here's the  link hbond.xvg file and its averaged file
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg



Neither of these files produce output that corresponds to the PNG image above. 
Both files have values in 6-9 H-bond range and thus agree with the g_analyze 
output, which I can reproduce.  I suspect you're somehow getting your files 
mixed up.


-Justin



On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta bharat.85.m...@gmail.comwrote:


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 jalem...@vt.edu 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 jalem...@vt.edu 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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--
==

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: Reaction field zero and ions

2013-11-11 Thread Williams Ernesto Miranda Delgado

Hello
If I did the MD simulation using PME and neutralized with ions, and I want
to rerun this time with reaction field zero, is there any problem if I
keep the ions? This is for LIE calculation. I am using AMBER99SB.
Thanks
Williams

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

2013-11-10 Thread Mark Abraham

 that is practical (but
I don't even know how many atoms you are simulating!)

Mark


Core t (s)   Wall t (s)(%)
Time:   178961.45022398.880  799.0
  6h13:18
  (ns/day)(hour/ns)
 Performance:   38.5730.622






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[gmx-users] Re: choosing force field

2013-11-10 Thread 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] http://user/SendEmail.jtp?type=nodenode=5012376i=0
 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
 
  --
  ==
 
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  Postdoctoral Fellow
 
  Department of Pharmaceutical Sciences
  School of Pharmacy
  Health Sciences Facility II, Room 601
  University of Maryland, Baltimore
  20 Penn St.
  Baltimore, MD 21201
 
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Re: [gmx-users] Re: g_analyze




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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Re: [gmx-users] Re: g_analyze

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 jalem...@vt.edu 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] Re: Thankful

2013-11-10 Thread 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




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

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 jalem...@vt.edu 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




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

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 jalem...@vt.edu 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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Re: [gmx-users] Re: g_analyze




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 jalem...@vt.edu 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

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 jalem...@vt.edu 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 jalem...@vt.edu 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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Re: [gmx-users] Re: choosing force field

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]
ml-node+s5086n5012325...@n6.nabble.com 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

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

--
==

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Postdoctoral Fellow

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

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

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Re: [gmx-users] Re: Ligand simulation for LIE with PME




On 11/8/13 3:32 PM, Williams Ernesto Miranda Delgado wrote:

Greetings again
If I use a salt concentration for neutralizing the protein-ligand complex
and run MD using PME, and the ligand is neutral, do I perform ligand MD
simulation without adding any salt concentration? It could be relevant for
LIE free energy calculation if I don't include salt in ligand (neutral)
simulation, even when I simulate Protein-ligand system with salt?


My assumption would be that you should introduce as few differences as possible. 
 Consider what LIE is doing - it is attempting to estimate the free energy of 
binding from simple interaction energies.  If you determine the strength of the 
ligand-protein interaction in the presence of some higher ionic strength medium, 
and then determine only the strength of ligand-water interactions rather than 
the interaction of the ligand with the same medium, then I'd say the calculation 
is flawed.  Think of what is really happening in real life - the ligand has to 
partition out of the solvent and into the protein's binding site.  The solvent 
is uniform throughout that process.


-Justin

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

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[gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-09 Thread rajat desikan

Hi Justin,
I take it that both the sets of parameters should produce identical
macroscopic quantities.
For the GPU, is this a decent .mdp?

cutoff-scheme= Verlet
vdwtype = switch
rlist= 1.2
;rlistlong = 1.4 NOT USED IN GPU...IS THIS
OK?
rvdw   = 1.2
;rvdw-switch= 1.0NOT USED IN GPU...IS THIS OK?
coulombtype   = pme
DispCorr = EnerPres
rcoulomb= 1.2


On Fri, Nov 8, 2013 at 7:19 PM, Justin Lemkul [via GROMACS] 
ml-node+s5086n5012351...@n6.nabble.com wrote:



 On 11/7/13 11:32 PM, Rajat Desikan wrote:

  Dear All,
  The setting that I mentioned above are from Klauda et al., for a POPE
  membrane system. They can be found in charmm_npt.mdp in lipidbook (link
  below)
  http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html
 
  Is there any reason not to use their .mdp parameters for a
 membrane-protein
  system? Justin's recommendation is highly valued since I am using his
  forcefield. Justin, your comments please
 

 Careful now, it's not my forcefield.  I derived only a very small part
 of it :)

  To summarize:
  Klauda et al., suggest
  rlist  = 1.0
  rlistlong= 1.4
  rvdw_switch  = 0.8
  vdwtype= Switch
  coulombtype  = pme
  DispCorr= EnerPres ;only usefull with reaction-field
  and pme or pppm
  rcoulomb   = 1.0
  rcoulomb_switch= 0.0
  rvdw = 1.2
 
  Justin's recommendation (per mail above)
  vdwtype = switch
  rlist = 1.2
  rlistlong = 1.4
  rvdw = 1.2
  rvdw-switch = 1.0
  rcoulomb = 1.2
 

 The differences between these two sets of run parameters are very small,
 dealing
 mostly with Coulomb and neighbor searching cutoffs.  I would suspect that
 any
 difference between simulations run with these two settings would be
 similarly
 small or nonexistent, given that rcoulomb is a bit flexible when using
 PME.  The
 value of rlist is rarely mentioned in papers, so it is good that the
 authors
 have provided the actual input file.  Previous interpretation of CHARMM
 usage
 generally advised setting rcoulomb = 1.2 to remain consistent with the
 original
 switching/shifting functions.  That setting becomes a bit less stringent
 when
 using PME.

 -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] http://user/SendEmail.jtp?type=nodenode=5012351i=0 |
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-- 
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] Re: CHARMM .mdp settings for GPU




On 11/9/13 4:16 PM, rajat desikan wrote:

Hi Justin,
I take it that both the sets of parameters should produce identical
macroscopic quantities.
For the GPU, is this a decent .mdp?

cutoff-scheme= Verlet
vdwtype = switch
rlist= 1.2
;rlistlong = 1.4 NOT USED IN GPU...IS THIS
OK?
rvdw   = 1.2
;rvdw-switch= 1.0NOT USED IN GPU...IS THIS OK?
coulombtype   = pme
DispCorr = EnerPres
rcoulomb= 1.2



I have no basis for saying whether or not it will produce correct results.  I 
have never tested this force field on GPU with the Verlet scheme.  My biggest 
concern is with the treatment of van der Waals interactions, and I have not used 
the Verlet scheme enough to understand what it is doing and how it will treat 
the interactions that should be switched.  If someone else can comment, that 
would be useful to me, as well!


Test carefully and please report back.  A comparison between CPU and GPU would 
be very valuable.


-Justin



On Fri, Nov 8, 2013 at 7:19 PM, Justin Lemkul [via GROMACS] 
ml-node+s5086n5012351...@n6.nabble.com wrote:




On 11/7/13 11:32 PM, Rajat Desikan wrote:


Dear All,
The setting that I mentioned above are from Klauda et al., for a POPE
membrane system. They can be found in charmm_npt.mdp in lipidbook (link
below)
http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html

Is there any reason not to use their .mdp parameters for a

membrane-protein

system? Justin's recommendation is highly valued since I am using his
forcefield. Justin, your comments please



Careful now, it's not my forcefield.  I derived only a very small part
of it :)


To summarize:
Klauda et al., suggest
rlist  = 1.0
rlistlong= 1.4
rvdw_switch  = 0.8
vdwtype= Switch
coulombtype  = pme
DispCorr= EnerPres ;only usefull with reaction-field
and pme or pppm
rcoulomb   = 1.0
rcoulomb_switch= 0.0
rvdw = 1.2

Justin's recommendation (per mail above)
vdwtype = switch
rlist = 1.2
rlistlong = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2



The differences between these two sets of run parameters are very small,
dealing
mostly with Coulomb and neighbor searching cutoffs.  I would suspect that
any
difference between simulations run with these two settings would be
similarly
small or nonexistent, given that rcoulomb is a bit flexible when using
PME.  The
value of rlist is rarely mentioned in papers, so it is good that the
authors
have provided the actual input file.  Previous interpretation of CHARMM
usage
generally advised setting rcoulomb = 1.2 to remain consistent with the
original
switching/shifting functions.  That setting becomes a bit less stringent
when
using PME.

-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] http://user/SendEmail.jtp?type=nodenode=5012351i=0 |
(410) 706-7441

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

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[gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-09 Thread Gianluca Interlandi

On Sat, 9 Nov 2013, Gianluca Interlandi wrote:

Just to chime in. Here is a that paper might be helpful in understanding
the role of cuoffs in the CHARMM force field:

AU STEINBACH, PJ
BROOKS, BR
AF STEINBACH, PJ
BROOKS, BR
TI NEW SPHERICAL-CUTOFF METHODS FOR LONG-RANGE FORCES IN MACROMOLECULAR
SIMULATION
SO JOURNAL OF COMPUTATIONAL CHEMISTRY
SN 0192-8651
PD JUL
PY 1994
VL 15
IS 7
BP 667
EP 683
DI 10.1002/jcc.540150702
UT WOS:A1994NU1741

Gianluca

On Sat, 9 Nov 2013, Justin Lemkul wrote:

On 11/9/13 4:16 PM, rajat desikan wrote:

Hi Justin,
I take it that both the sets of parameters should produce identical
macroscopic quantities.
For the GPU, is this a decent .mdp?

cutoff-scheme= Verlet
vdwtype = switch
rlist= 1.2
;rlistlong = 1.4 NOT USED IN GPU...IS THIS
OK?
rvdw = 1.2
;rvdw-switch= 1.0NOT USED IN GPU...IS THIS OK?
coulombtype = pme
DispCorr = EnerPres
rcoulomb= 1.2

I have no basis for saying whether or not it will produce correct results.
I have never tested this force field on GPU with the Verlet scheme. My
biggest concern is with the treatment of van der Waals interactions, and I
have not used the Verlet scheme enough to understand what it is doing and
how it will treat the interactions that should be switched. If someone
else can comment, that would be useful to me, as well!

Test carefully and please report back. A comparison between CPU and GPU
would be very valuable.

-Justin

On Fri, Nov 8, 2013 at 7:19 PM, Justin Lemkul [via GROMACS]
ml-node+s5086n5012351...@n6.nabble.com wrote:

On 11/7/13 11:32 PM, Rajat Desikan wrote:

Dear All,
The setting that I mentioned above are from Klauda et al., for a POPE
membrane system. They can be found in charmm_npt.mdp in lipidbook (link
below)
http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html

Is there any reason not to use their .mdp parameters for a

membrane-protein

system? Justin's recommendation is highly valued since I am using his
forcefield. Justin, your comments please

Careful now, it's not my forcefield. I derived only a very small part
of it :)

To summarize:
Klauda et al., suggest
rlist = 1.0
rlistlong= 1.4
rvdw_switch = 0.8
vdwtype= Switch
coulombtype = pme
DispCorr= EnerPres ;only usefull with reaction-field
and pme or pppm
rcoulomb = 1.0
rcoulomb_switch= 0.0
rvdw = 1.2

Justin's recommendation (per mail above)
vdwtype = switch
rlist = 1.2
rlistlong = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2

The differences between these two sets of run parameters are very small,
dealing
mostly with Coulomb and neighbor searching cutoffs. I would suspect that
any
difference between simulations run with these two settings would be
similarly
small or nonexistent, given that rcoulomb is a bit flexible when using
PME. The
value of rlist is rarely mentioned in papers, so it is good that the
authors
have provided the actual input file. Previous interpretation of CHARMM
usage
generally advised setting rcoulomb = 1.2 to remain consistent with the
original
switching/shifting functions. That setting becomes a bit less stringent
when
using PME.

-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] http://user/SendEmail.jtp?type=nodenode=5012351i=0 |
(410) 706-7441

==
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Re: [gmx-users] Re: CHARMM .mdp settings for GPU




On 11/9/13 9:51 PM, Gianluca Interlandi wrote:

On Sat, 9 Nov 2013, Gianluca Interlandi wrote:

Just to chime in. Here is a that paper might be helpful in understanding the
role of cuoffs in the CHARMM force field:

AU STEINBACH, PJ
BROOKS, BR
AF STEINBACH, PJ
BROOKS, BR
TI NEW SPHERICAL-CUTOFF METHODS FOR LONG-RANGE FORCES IN MACROMOLECULAR
SIMULATION
SO JOURNAL OF COMPUTATIONAL CHEMISTRY
SN 0192-8651
PD JUL
PY 1994
VL 15
IS 7
BP 667
EP 683
DI 10.1002/jcc.540150702
UT WOS:A1994NU1741


Yes, that's the one I posted several weeks back.  It describes the original 
implementation of cutoff schemes in CHARMM.


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

2013-11-09 Thread Dwey Kauffman

!


NOTE: The GPU has 20% more load than the CPU. This imbalance causes
  performance loss, consider using a shorter cut-off and a finer PME
grid.

   Core t (s)   Wall t (s)(%)
   Time:   216205.51027036.812  799.7
 7h30:36
 (ns/day)(hour/ns)
Performance:   31.9560.751


### Two GPUs #

 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   %
-
 Domain decomp. 24 10 339.49010900.191 1.5
 DD comm. load  24  49989   0.2628.410 0.0
 Neighbor search24 11 481.58315462.464 2.2
 Launch GPU ops.24   1002 579.28318599.358 2.6
 Comm. coord.   24490 523.09616795.351 2.3
 Force  245011545.58449624.951 6.9
 Wait + Comm. F 24501 821.74026384.083 3.7
 PME mesh   24501   11097.880   356326.03049.5
 Wait GPU nonlocal  245011001.86832167.550 4.5
 Wait GPU local 24501   8.613  276.533 0.0
 NB X/F buffer ops. 24   19821061.23834073.781 4.7
 Write traj.24   1025   5.681  182.419 0.0
 Update 245011692.23354333.503 7.6
 Constraints245012316.14574365.78810.3
 Comm. energies 24101  15.802  507.373 0.1
 Rest   2 908.38329165.963 4.1
-
 Total  2   22398.880   719173.747   100.0
-
-
 PME redist. X/F24   10021519.28848780.654 6.8
 PME spread/gather  24   10025398.693   173338.93624.1
 PME 3D-FFT 24   10022798.48289852.48212.5
 PME 3D-FFT Comm.   24   1002 947.03330406.937 4.2
 PME solve  24501 420.66713506.611 1.9
-

   Core t (s)   Wall t (s)(%)
   Time:   178961.45022398.880  799.0
 6h13:18
 (ns/day)(hour/ns)
Performance:   38.5730.622






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[gmx-users] Re: g_analyze

2013-11-09 Thread bharat gupta

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.

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 ??

Please clarify these doubts..

Regards

Bharat
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Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-08 Thread Justin Lemkul




On 11/7/13 11:32 PM, Rajat Desikan wrote:

Dear All,
The setting that I mentioned above are from Klauda et al., for a POPE
membrane system. They can be found in charmm_npt.mdp in lipidbook (link
below)
http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html

Is there any reason not to use their .mdp parameters for a membrane-protein
system? Justin's recommendation is highly valued since I am using his
forcefield. Justin, your comments please



Careful now, it's not my forcefield.  I derived only a very small part of it 
:)


To summarize:
Klauda et al., suggest
rlist  = 1.0
rlistlong= 1.4
rvdw_switch  = 0.8
vdwtype= Switch
coulombtype  = pme
DispCorr= EnerPres ;only usefull with reaction-field
and pme or pppm
rcoulomb   = 1.0
rcoulomb_switch= 0.0
rvdw = 1.2

Justin's recommendation (per mail above)
vdwtype = switch
rlist = 1.2
rlistlong = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2



The differences between these two sets of run parameters are very small, dealing 
mostly with Coulomb and neighbor searching cutoffs.  I would suspect that any 
difference between simulations run with these two settings would be similarly 
small or nonexistent, given that rcoulomb is a bit flexible when using PME.  The 
value of rlist is rarely mentioned in papers, so it is good that the authors 
have provided the actual input file.  Previous interpretation of CHARMM usage 
generally advised setting rcoulomb = 1.2 to remain consistent with the original 
switching/shifting functions.  That setting becomes a bit less stringent when 
using PME.


-Justin

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[gmx-users] Re: free energy

2013-11-08 Thread kghm

Dear Kieu Thu 

Thanks for your comment about free energy. Unfortunately, I could not send a
email to Paissoni Cristina in the Gromacs Forum.
Could you give me email address of Paissoni Cristina? Finding a tool for
calculation MM/PBSA with Gromacs is very vital for me.

Best Regards
Kiana

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[gmx-users] Re: Ligand simulation for LIE with PME

2013-11-08 Thread Williams Ernesto Miranda Delgado

Greetings again
If I use a salt concentration for neutralizing the protein-ligand complex
and run MD using PME, and the ligand is neutral, do I perform ligand MD
simulation without adding any salt concentration? It could be relevant for
LIE free energy calculation if I don't include salt in ligand (neutral)
simulation, even when I simulate Protein-ligand system with salt?
Thanks

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[gmx-users] Re: choosing force field

2013-11-08 Thread pratibha

Sorry for the previous mistake. Instead of 53a7, the force field which I
used was 53a6.

On Fri, Nov 8, 2013 at 12:10 AM, Justin Lemkul [via GROMACS]
ml-node+s5086n5012325...@n6.nabble.com 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?

-Justin

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University of Maryland, Baltimore
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Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs

First, there is no value in ascribing problems to the hardware if the
simulation setup is not yet balanced, or not large enough to provide enough
atoms and long enough rlist to saturate the GPUs, etc. Look at the log
files and see what complaints mdrun makes about things like PME load
balance, and the times reported for different components of the simulation,
because these must differ between the two runs you report. diff -y -W 160
*log |less is your friend. Some (non-GPU-specific) background information
in part 5 here
http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/Topology_preparation%2c_%22What's_in_a_log_file%22%2c_basic_performance_improvements%3a_Mark_Abraham%2c_Session_1A
(though
I recommend the PDF version)

Mark

On Thu, Nov 7, 2013 at 6:34 AM, James Starlight jmsstarli...@gmail.comwrote:

I've gone to conclusion that simulation with 1 or 2 GPU simultaneously gave
me the same performance
mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v -deffnm md_CaM_test,

mdrun -ntmpi 2 -ntomp 6 -gpu_id 0 -v -deffnm md_CaM_test,

Doest it be due to the small CPU cores or addition RAM ( this system has 32
gb) is needed ? OR may be some extra options are needed in the config?

James

2013/11/6 Richard Broadbent richard.broadben...@imperial.ac.uk

Hi Dwey,

On 05/11/13 22:00, Dwey Kauffman wrote:

Hi Szilard,

Thanks for your suggestions. I am indeed aware of this page. In a
8-core
AMD with 1GPU, I am very happy about its performance. See below. My
intention is to obtain a even better one because we have multiple nodes.

### 8 core AMD with 1 GPU,
Force evaluation time GPU/CPU: 4.006 ms/2.578 ms = 1.554
For optimal performance this ratio should be close to 1!

NOTE: The GPU has 20% more load than the CPU. This imbalance causes
performance loss, consider using a shorter cut-off and a finer
PME
grid.

Core t (s) Wall t (s)(%)
Time: 216205.51027036.812 799.7
7h30:36
(ns/day)(hour/ns)
Performance: 31.9560.751

### 8 core AMD with 2 GPUs

Core t (s) Wall t (s)(%)
Time: 178961.45022398.880 799.0
6h13:18
(ns/day)(hour/ns)
Performance: 38.5730.622
Finished mdrun on node 0 Sat Jul 13 09:24:39 2013

I'm almost certain that Szilard meant the lines above this that give the
breakdown of where the time is spent in the simulation.

Richard

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.

OK but can you give a example of mdrun command ? given a 8 core AMD
with 2
GPUs.
I will try to run it again.

Regarding scaling across nodes, you can't expect much from gigabit
ethernet - especially not from the cheaper cards/switches, 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). However, on infiniband clusters we
have seen scaling to 100 atoms/core (at peak).

From your comments, it sounds like a cluster of AMD cpus is difficult
to

scale across nodes in our current setup.

Let's assume we install Infiniband (20 or 40GB/s) in the same system of
16
nodes of 8 core AMD with 1 GPU only. Considering the same AMD system,
what
is a good way to obtain better performance when we run a task across
nodes
? in other words, what dose mudrun_mpi look like ?

Thanks,
Dwey

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Re: [gmx-users] Re: single point calculation with gromacs

On Wed, Nov 6, 2013 at 4:07 PM, fantasticqhl fantastic...@gmail.com wrote:

Dear Justin,

I am sorry for the late reply. I still can't figure it out.

It isn't rocket science - your two .mdp files describe totally different
model physics. To compare things, change as few things as necessary to
generate the comparison. So use the same input .mdp file for the MD vs EM
single-point comparison, just changing the integrator line, and maybe
unconstrained-start (I forget the details). And be aware of
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy

Mark

Could you please send me the mdp file which was used for your single point
calculations.
I want to do some comparison and then solve the problem.
Thanks very much!

All the best,
Qinghua

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[gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-07 Thread Rajat Desikan

Dear All,

Any suggestions? 

Thank you.

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Re: [gmx-users] Re: CHARMM .mdp settings for GPU

Hi,

It's not easy to be explicit. CHARMM wasn't parameterized with PME, so the
original paper's coulomb settings can be taken with a grain of salt for use
with PME - others' success in practice should be a guideline here. The good
news is that the default GROMACS PME settings are pretty good for at least
some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and the GPU
auto-tuning of parameters in 4.6 is designed to preserve the right sorts of
things.

LJ is harder because it would make good sense to preserve the way CHARMM
did it, but IIRC you can't use something equivalent to the CHARMM LJ shift
with the Verlet kernels, either natively or with a table. We hope to fix
that in 5.0, but code is not written yet. I would probably use vdwtype =
cut-off, vdw-modifier = potential-shift-verlet and rcoulomb=rlist=rvdw=1.2,
but I don't run CHARMM simulations for a living ;-)

Mark


On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan rajatdesi...@gmail.comwrote:

 Dear All,

 Any suggestions?

 Thank you.

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[gmx-users] Re: choosing force field

2013-11-07 Thread pratibha

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?  
Thanks in advance.

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Re: [gmx-users] Re: choosing force field

2013-11-07 Thread Justin Lemkul




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

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[gmx-users] Re: LIE method with PME

2013-11-07 Thread Williams Ernesto Miranda Delgado

Hello
I performed MD simulations of several Protein-ligand complexes and
solvated Ligands using PME for log range electrostatics. I want to
calculate the binding free energy using the LIE method, but when using
g_energy I only get Coul-SR. How can I deal with Ligand-environment long
range electrostatic interaction using gromacs? I have seen other
discussion lists but I couldn't arrive to a solution. Could you please
help me?
Thank you
Williams


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Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-07 Thread rajat desikan

Thank you, Mark. I think that running it on CPUs is a safer choice at
present.


On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham mark.j.abra...@gmail.comwrote:

 Hi,

 It's not easy to be explicit. CHARMM wasn't parameterized with PME, so the
 original paper's coulomb settings can be taken with a grain of salt for use
 with PME - others' success in practice should be a guideline here. The good
 news is that the default GROMACS PME settings are pretty good for at least
 some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and the GPU
 auto-tuning of parameters in 4.6 is designed to preserve the right sorts of
 things.

 LJ is harder because it would make good sense to preserve the way CHARMM
 did it, but IIRC you can't use something equivalent to the CHARMM LJ shift
 with the Verlet kernels, either natively or with a table. We hope to fix
 that in 5.0, but code is not written yet. I would probably use vdwtype =
 cut-off, vdw-modifier = potential-shift-verlet and rcoulomb=rlist=rvdw=1.2,
 but I don't run CHARMM simulations for a living ;-)

 Mark


 On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan rajatdesi...@gmail.com
 wrote:

  Dear All,
 
  Any suggestions?
 
  Thank you.
 
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-- 
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] Re: CHARMM .mdp settings for GPU

Reasonable, but CPU-only is not 100% conforming either; IIRC the CHARMM
switch differs from the GROMACS switch (Justin linked a paper here with the
CHARMM switch description a month or so back, but I don't have that link to
hand).

Mark


On Thu, Nov 7, 2013 at 8:45 PM, rajat desikan rajatdesi...@gmail.comwrote:

 Thank you, Mark. I think that running it on CPUs is a safer choice at
 present.


 On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

  Hi,
 
  It's not easy to be explicit. CHARMM wasn't parameterized with PME, so
 the
  original paper's coulomb settings can be taken with a grain of salt for
 use
  with PME - others' success in practice should be a guideline here. The
 good
  news is that the default GROMACS PME settings are pretty good for at
 least
  some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and the
 GPU
  auto-tuning of parameters in 4.6 is designed to preserve the right sorts
 of
  things.
 
  LJ is harder because it would make good sense to preserve the way CHARMM
  did it, but IIRC you can't use something equivalent to the CHARMM LJ
 shift
  with the Verlet kernels, either natively or with a table. We hope to fix
  that in 5.0, but code is not written yet. I would probably use vdwtype =
  cut-off, vdw-modifier = potential-shift-verlet and
 rcoulomb=rlist=rvdw=1.2,
  but I don't run CHARMM simulations for a living ;-)
 
  Mark
 
 
  On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan rajatdesi...@gmail.com
  wrote:
 
   Dear All,
  
   Any suggestions?
  
   Thank you.
  
   --
   View this message in context:
  
 
 http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html
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 Prof. K. Ganapathy Ayappa's Lab (no 13),
 Dept. of Chemical Engineering,
 Indian Institute of Science, Bangalore
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Re: [gmx-users] Re: LIE method with PME

If the long-range component of your electrostatics model is not
decomposable by group (which it isn't), then you can't use that with LIE.
See the hundreds of past threads on this topic :-)

Mark


On Thu, Nov 7, 2013 at 8:34 PM, Williams Ernesto Miranda Delgado 
wmira...@fbio.uh.cu wrote:

 Hello
 I performed MD simulations of several Protein-ligand complexes and
 solvated Ligands using PME for log range electrostatics. I want to
 calculate the binding free energy using the LIE method, but when using
 g_energy I only get Coul-SR. How can I deal with Ligand-environment long
 range electrostatic interaction using gromacs? I have seen other
 discussion lists but I couldn't arrive to a solution. Could you please
 help me?
 Thank you
 Williams


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Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-07 Thread Gianluca Interlandi


Hi Mark!

I think that this is the paper that you are referring to:

dx.doi.org/10.1021/ct900549r

Also for your reference, these are the settings that Justin recommended 
using with CHARMM in gromacs:


vdwtype = switch
rlist = 1.2
rlistlong = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2

As you mention the switch function in gromacs is different than in CHARMM 
but it appears that the difference is very small.


Gianluca

On Thu, 7 Nov 2013, Mark Abraham wrote:


Reasonable, but CPU-only is not 100% conforming either; IIRC the CHARMM
switch differs from the GROMACS switch (Justin linked a paper here with the
CHARMM switch description a month or so back, but I don't have that link to
hand).

Mark


On Thu, Nov 7, 2013 at 8:45 PM, rajat desikan rajatdesi...@gmail.comwrote:


Thank you, Mark. I think that running it on CPUs is a safer choice at
present.


On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham mark.j.abra...@gmail.com

wrote:



Hi,

It's not easy to be explicit. CHARMM wasn't parameterized with PME, so

the

original paper's coulomb settings can be taken with a grain of salt for

use

with PME - others' success in practice should be a guideline here. The

good

news is that the default GROMACS PME settings are pretty good for at

least

some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and the

GPU

auto-tuning of parameters in 4.6 is designed to preserve the right sorts

of

things.

LJ is harder because it would make good sense to preserve the way CHARMM
did it, but IIRC you can't use something equivalent to the CHARMM LJ

shift

with the Verlet kernels, either natively or with a table. We hope to fix
that in 5.0, but code is not written yet. I would probably use vdwtype =
cut-off, vdw-modifier = potential-shift-verlet and

rcoulomb=rlist=rvdw=1.2,

but I don't run CHARMM simulations for a living ;-)

Mark


On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan rajatdesi...@gmail.com

wrote:



Dear All,

Any suggestions?

Thank you.

--
View this message in context:




http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html

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Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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mdrun on 8-core AMD + GTX TITAN (was: Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs)

2013-11-07 Thread Szilárd Páll

Let's not hijack James' thread as your hardware is different from his.

On Tue, Nov 5, 2013 at 11:00 PM, Dwey Kauffman mpi...@gmail.com wrote:
 Hi Szilard,

Thanks for your suggestions. I am  indeed aware of this page. In a 8-core
 AMD with 1GPU, I am very happy about its performance. See below. My

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.

 intention is to obtain a even better one because we have multiple nodes.

Btw, I'm not sure it's an economically viable solution to install
Infiniband network - especially if you have desktop-class machines.
Such a network will end up costing $500 per machine just for a single
network card, let alone cabling and switches.


 ### 8 core AMD with  1 GPU,
 Force evaluation time GPU/CPU: 4.006 ms/2.578 ms = 1.554
 For optimal performance this ratio should be close to 1!


 NOTE: The GPU has 20% more load than the CPU. This imbalance causes
   performance loss, consider using a shorter cut-off and a finer PME
 grid.

Core t (s)   Wall t (s)(%)
Time:   216205.51027036.812  799.7
  7h30:36
  (ns/day)(hour/ns)
 Performance:   31.9560.751

 ### 8 core AMD with 2 GPUs

Core t (s)   Wall t (s)(%)
Time:   178961.45022398.880  799.0
  6h13:18
  (ns/day)(hour/ns)
 Performance:   38.5730.622
 Finished mdrun on node 0 Sat Jul 13 09:24:39 2013


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.

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.


 OK but can you give a example of mdrun command ? given a 8 core AMD with 2
 GPUs.
 I will try to run it again.

You could try running
mpirun -np 4 mdrun -ntomp 2 -gpu_id 0011
but I suspect this won't help because your scaling issue



Regarding scaling across nodes, you can't expect much from gigabit
ethernet - especially not from the cheaper cards/switches, 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). However, on infiniband clusters we
have seen scaling to 100 atoms/core (at peak).

 From your comments, it sounds like a cluster of AMD cpus is difficult to
 scale across nodes in our current setup.

 Let's assume we install Infiniband (20 or 40GB/s) in the same system of 16
 nodes of 8 core AMD with 1 GPU only. Considering the same AMD system, what
 is a good way to obtain better performance  when we run a task across nodes
 ? in other words, what dose mudrun_mpi look like ?

 Thanks,
 Dwey




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Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs

2013-11-07 Thread Szilárd Páll

On Thu, Nov 7, 2013 at 6:34 AM, James Starlight jmsstarli...@gmail.com wrote:
 I've gone to conclusion that simulation with 1 or 2 GPU simultaneously gave
 me the same performance
 mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v  -deffnm md_CaM_test,

 mdrun -ntmpi 2 -ntomp 6 -gpu_id 0 -v  -deffnm md_CaM_test,

 Doest it be due to the small CPU cores or addition RAM ( this system has 32
 gb) is needed ? OR may be some extra options are needed in the config?

GROMACS does not really need much (or fast) ram and it's most probably
not configuration settings that are causing the lack of scaling.

Given your setup my guess is that your hardware for your system is
simply imbalanced to be efficiently used in GROMACS runs.

Please post *full* log files (FYI use e.g. http://pastebin.com), that
will help explain what is going on.


 James




 2013/11/6 Richard Broadbent richard.broadben...@imperial.ac.uk

 Hi Dwey,


 On 05/11/13 22:00, Dwey Kauffman wrote:

 Hi Szilard,

 Thanks for your suggestions. I am  indeed aware of this page. In a
 8-core
 AMD with 1GPU, I am very happy about its performance. See below. My
 intention is to obtain a even better one because we have multiple nodes.

 ### 8 core AMD with  1 GPU,
 Force evaluation time GPU/CPU: 4.006 ms/2.578 ms = 1.554
 For optimal performance this ratio should be close to 1!


 NOTE: The GPU has 20% more load than the CPU. This imbalance causes
performance loss, consider using a shorter cut-off and a finer PME
 grid.

 Core t (s)   Wall t (s)(%)
 Time:   216205.51027036.812  799.7
   7h30:36
   (ns/day)(hour/ns)
 Performance:   31.9560.751

 ### 8 core AMD with 2 GPUs

 Core t (s)   Wall t (s)(%)
 Time:   178961.45022398.880  799.0
   6h13:18
   (ns/day)(hour/ns)
 Performance:   38.5730.622
 Finished mdrun on node 0 Sat Jul 13 09:24:39 2013


 I'm almost certain that Szilard meant the lines above this that give the
 breakdown of where the time is spent in the simulation.

 Richard


  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.



 OK but can you give a example of mdrun command ? given a 8 core AMD with 2
 GPUs.
 I will try to run it again.


  Regarding scaling across nodes, you can't expect much from gigabit
 ethernet - especially not from the cheaper cards/switches, 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). However, on infiniband clusters we
 have seen scaling to 100 atoms/core (at peak).


  From your comments, it sounds like a cluster of AMD cpus is difficult to

 scale across nodes in our current setup.

 Let's assume we install Infiniband (20 or 40GB/s) in the same system of 16
 nodes of 8 core AMD with 1 GPU only. Considering the same AMD system, what
 is a good way to obtain better performance  when we run a task across
 nodes
 ? in other words, what dose mudrun_mpi look like ?

 Thanks,
 Dwey




 --
 View this message in context: http://gromacs.5086.x6.nabble.
 com/Gromacs-4-6-on-two-Titans-GPUs-tp5012186p5012279.html
 Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

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[gmx-users] Re: LIE method with PME

2013-11-07 Thread Williams Ernesto Miranda Delgado

Thank you Mark
What do you think about making a rerun on the trajectories generated
previously with PME but this time using coulombtype: cut-off? Could you
suggest a cut off value?
Thanks again
Williams

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Re: [gmx-users] Re: LIE method with PME