[gmx-users] Error in REMD

[Nikunj Maheshwari]

Dear all...

We ran REMD simulations for 36 replicas. We got an error which stopped the
whole simulation.

"
Reading file md21.tpr, VERSION 4.5.5 (single precision)
Loaded with Money

Reading file md24.tpr, VERSION 4.5.5 (single precision)
Loaded with Money


---
Program mdrun_mpi, VERSION 4.5.5
Source code file: symtab.c, line: 108

Fatal error:
symtab get_symtab_handle 1031126655 not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"The World is a Friendly Place" (Magnapop)

Error on node 35, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 35 out of 36

gcq#103: "The World is a Friendly Place" (Magnapop)

MPI: Global rank 35 is aborting with error code -1.
"

Can someone help us in knowing what the error means and how to it can be
rectified?

Thanks
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Re: [gmx-users] Mismatching number of PP MPI processes and GPUs per node

[George Patargias]

Hello Szilard

Many thanks for these very useful comments!

We run jobs on a single node of a small Apple cluster (no Infiniband
unfortunately). One node has two Intel(R) Xeon(R) X5650 Processors each
with 6 cores and 12 threads, so in total 12 cores and 24 threads.

I have compiled GROMACS 4.6.1 with OpenMP and CUDA support (-DGMX_MPI=OFF)

Do I understand correctly that this build will work efficiently without gpu
but not with gpu as you mention?

In order to run gromacs according to your suggestion

mpirun -np 2 -ntomp 6 mdrun_mpi -s test.tpr -deffnm test_out -gpu_id 00

Do I need to compile with MPI (i.e. -DGMX_MPI=ON)?

Would this then be the most efficient way to run GROMACS in the given
hardware set-up (dual socket, total 12 cores and GPU)?

Thanks again!

Best
George




> FYI: On your machine running OpenMP across two sockets will probably not be
> very efficient. Depending on the input and at how high paralleliation
are
> you running, you could be better off with running multiple MPI ranks per
GPU. This is a bit of an unexplained feature due to it being complicated
to
> use and not fully supported (does not woth with thread-MPI), but you can
essentially make  multiple MPI ranks use the same GPU by passing the ID
of
> the GPU you want to "overload" multiple times (and launching the correct
number of MPI ranks).
> For instance, in your case you can try putting one MPI rank per socket,
both using GPU 0 by:
> mpirun -np 2 -ntomp 6 mdrun_mpi -s test.tpr -deffnm test_out -nb gpu
-gpu_id 00
> This is briefly explained on the wiki as well:
> http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multiple_MPI_ranks_per_GPU
Let us know whether you are able to get useful speedup from GPUs!
Cheers,
> --
> Szil?rd
> On Tue, Mar 12, 2013 at 10:06 AM, George Patargias
> wrote:
>> Hi Carsten
>> Thanks a lot for this tip. It worked!
>> George
>> > Hi,
>> > On Mar 11, 2013, at 10:50 AM, George Patargias 
>> wrote:
>> >> Hello
>> >> Sorry for posting this again.
>> >> I am trying to run GROMACS 4.6 compiled with MPI and GPU
acceleration
>> >> (CUDA 5.0 lib) using the following SGE batch script.
>> >> #!/bin/sh
>> >> #$ -V
>> >> #$ -S /bin/sh
>> >> #$ -N test-gpus
>> >> #$ -l h="xgrid-node02"
>> >> #$ -pe mpi_fill_up 12
>> >> #$ -cwd
>> >> source /opt/NetUsers/pgkeka/gromacs-4.6_gpu_mpi/bin/GMXRC
>> >> export
>> >> DYLD_LIBRARY_PATH=/Developer/NVIDIA/CUDA-5.0/lib:$DYLD_LIBRARY_PATH
mpirun -np 12 mdrun_mpi -s test.tpr -deffnm test_out -nb gpu After
detection of the installed GPU card
>> >> 1 GPU detected on host xgrid-node02.xgrid:
>> >>  #0: NVIDIA Quadro 4000, compute cap.: 2.0, ECC:  no, stat:
>> compatible
>> >> GROMACS issues the following error
>> >> Incorrect launch configuration: mismatching number of PP MPI
>> processes
>> >> and
>> >> GPUs per node. mdrun_mpi was started with 12 PP MPI processes per
>> node,
>> >> but only 1 GPU were detected.
>> >> It can't be that we need to run GROMACS only on a single core so
that
>> it
>> >> matches the single GPU card.
>> > Have you compiled mdrun_mpi with OpenMP threads support? Then, if you do
>> > mpirun -np 1 mdrun_mpi ?
>> > it should start one MPI process with 12 OpenMP threads, which should
>> give
>> > you what you want. You can also manually specify the number of OpenMP
threads
>> > by adding
>> > -ntomp 12
>> > Carsten
>> >> Do you have any idea what has to be done?
>> >> Many thanks.
>> >> Dr. George Patargias
>> >> Postdoctoral Researcher
>> >> Biomedical Research Foundation
>> >> Academy of Athens
>> >> 4, Soranou Ephessiou
>> >> 115 27
>> >> Athens
>> >> Greece
>> >> Office: +302106597568
>> >> --
>> >> 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!
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interface or send it to gmx-users-requ...@gromacs.org.
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > --
>> > Dr. Carsten Kutzner
>> > Max Planck Institute for Biophysical Chemistry
>> > Theoretical and Computational Biophysics
>> > Am Fassberg 11, 37077 Goettingen, Germany
>> > Tel. +49-551-2012313, Fax: +49-551-2012302
>> > http://www.mpibpc.mpg.de/grubmueller/kutzner
>> > http://www.mpibpc.mpg.de/grubmueller/sppexa
>> > --
>> > gmx-users mailing listgmx-users@gromacs.org
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>> Dr. George Patargias
>> Postdoctoral Researcher
>> Biomedical Research Foundation
>> Academy of Athens
>> 4, Soranou Ephessiou
>> 115 27
>> Athens
>> Greece
>> Office: +302106597568
>> --
>> gmx-users mail

[gmx-users] how can we obtain replicated trajectory?

[Albert]

Hello:

 I've finished a replica exchange simulation with 72 replica 
(300K-580K) under explicit solvent model. It generate 72 trajectory and 
the replica since to "cross" well with neighboring temperature. Here is 
the figure:



http://dl.dropbox.com/u/56271062/REMD.png

 I am just wondering how can we generate and visualize the system at 
300 K  with that at 400-500 K? There is a ligand in my system, and it is 
expected to escape binding pocket with large loop movement


thank you very much

best
Albert
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[gmx-users] proper and improper dihedrals in topology file from other ff

[라지브간디]

Dear Justin,


I got understand the gromos ff improper style. however, what i am asking here 
is how would i use the charmm/amber improper from literuatre where they 
indicate the improper in this was ( something X-X)




Improper 
> CPB-X-X-CR1E 90.0 0.0 
> CC - X-X-NB 18.3 0.0 
> 






What X shows here and how do i use this in gromos format way?







Every force field has small differences in format. Look at ffbonded.itp for 
43A1 and you will see #define statements that correspond to bonds (gb_*), 
angles 
(ga_*), etc. Those macros just mean "substitute this information here." It's 
shorthand. So either you can introduce a new definition in ffbonded.itp or just 
type the parameters in manually according to the format specified in the 
manual. 

-Justin 










Dear gmx users, 
> 
> 
> I am MD simulation for heme ligated protein where i given all bond and angle, 
> dihedral information in topology file created by pd2gmx ( gromos43a1). 
> 
> 
> However, i do not know how to interpret the proper and improper dihedrals in 
> topology file? I have looked over the .rtp file and found that gromos 
> mentioned like 
> 
> example: 
> 
> 
> [ impropers ] 
> ; ai aj ak al gromos type 
> C2 N1 N3 NA2 gi_1 
> NA2 HA21 HA22 C2 gi_1 
> N3 C2 C4 HA3 gi_1 
> 
> 
> But the the parameter I use from literature where its in charmm and amber 
> format as they mentioned the torsions like following way. 
> 
> 
> Improper 
> CPB-X-X-CR1E 90.0 0.0 
> CC - X-X-NB 18.3 0.0 
> 
> 
> ...etc 
> 
> 
> How do i use this improper to utilize in gromos? 
> 


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[gmx-users] Re: Re: help with chromophore of a GFP

[Anna MARABOTTI]

 
Dear Mark, Justin and other gmx-users,
 thank you very much for your
help. Thanks to your suggestions, I made some steps forward, but still I
don't see the end of my travel...

 First of all, I would like to say
that my previous problem was solved when I renamed O1 to OA. Justin was
right. When I did it, no other error messages came from pdb2gmx
(including the "long bond" warning). 

Now...let's go to the following
problem... :'( After pdb2gmx, editconf, genbox, here I am with grompp...
When I made it, the fatal error was a list of No default Bond types No
default angle types No default Proper Dih. types No default Improper
Dih. types all referred to CFY, obviously. I know what the problem is, I
don't know how to solve it. I did not add bonded types to ffbonded.itp
because I was sure they all were present. Instead, there are some bonds
that are not present. I have the parameters calculated for these bonds
by Antechamber suite, but I don't know how to convert their format to
the format required by ffbonded.itp. For example, this is the entry I
have for a CT-CT bond in the output coming from Antechamber: 

CT-CT
303.10 1.535 same as c3-c3 

and this is the entry for a CT-CT bond in
ffbonded.itp: 

CT CT 1 0.15260 259408.0 ; 7,(1986),230; AA, SUGARS 

I
can imagine that 1.535 and 0.15260 is the bond length (in A in the first
case, in nm in the second case) and they are more or less identical. But
how can I obtain the second value in ffbond.itp (the kb in kJ mol-1
nm-2) from the data I have? I don't recognize at all the value...

I
know that this is not strictly referred to Gromacs, anyway could you
please tell me at least how can I find information on how to add these
parameters properly? 

Anna


__
Anna Marabotti,
Ph.D.
Assistant Professor
Department of Chemistry and Biology
University
of Salerno
Via Ponte don Melillo
84084 Fisciano (SA)
Italy
Phone: +39
089 969583
Fax: +39 089 969603
E-mail: amarabo...@unisa.it
Skype:
annam1972

"When a man with a gun meets a man with a pen, the man with
the gun is a dead man"
(Roberto Benigni, about Roberto Saviano)
 Il
21/03/2013 21:53, gmx-users-requ...@gromacs.org [1] ha scritto: 




Links:
--
[1] mailto:gmx-users-requ...@gromacs.org
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Re: [gmx-users] Re: Re: help with chromophore of a GFP

[Mark Abraham]

On Fri, Mar 22, 2013 at 2:36 PM, Anna MARABOTTI  wrote:

>
> Dear Mark, Justin and other gmx-users,
>  thank you very much for your
> help. Thanks to your suggestions, I made some steps forward, but still I
> don't see the end of my travel...
>
>  First of all, I would like to say
> that my previous problem was solved when I renamed O1 to OA. Justin was
> right. When I did it, no other error messages came from pdb2gmx
> (including the "long bond" warning).
>

OK, that's doubly good news.

Now...let's go to the following
> problem... :'( After pdb2gmx, editconf, genbox, here I am with grompp...
> When I made it, the fatal error was a list of No default Bond types No
> default angle types No default Proper Dih. types No default Improper
> Dih. types all referred to CFY, obviously. I know what the problem is, I
> don't know how to solve it. I did not add bonded types to ffbonded.itp
> because I was sure they all were present. Instead, there are some bonds
> that are not present. I have the parameters calculated for these bonds
> by Antechamber suite, but I don't know how to convert their format to
> the format required by ffbonded.itp. For example, this is the entry I
> have for a CT-CT bond in the output coming from Antechamber:
>
> CT-CT
> 303.10 1.535 same as c3-c3
>
> and this is the entry for a CT-CT bond in
> ffbonded.itp:
>
> CT CT 1 0.15260 259408.0 ; 7,(1986),230; AA, SUGARS
>
> I
> can imagine that 1.535 and 0.15260 is the bond length (in A in the first
> case, in nm in the second case) and they are more or less identical. But
> how can I obtain the second value in ffbond.itp (the kb in kJ mol-1
> nm-2) from the data I have? I don't recognize at all the value...
>

You'll have to start with the Antechamber documentation to find out the use
of and dimensions for those numbers. I have no idea at all, but I'd not be
surprised to hear that it was kcal mol-1 A-2 and perhaps a stray factor of
2 missing from the equation in which it works. That would account for the
factor of ~800 you see here.

You have the option of editing ffbonded.itp (so the lookup from [bonds] is
done via the two atom numbers, which index into [atoms] to get the two atom
names, which index into [bondedtypes]) or on the relevant line of [bonds]
(just dumping the same function type and parameters you'd use in
ffbonded.itp). What to do depends how much you plan to re-use the output of
Antechamber.

Mark


> I
> know that this is not strictly referred to Gromacs, anyway could you
> please tell me at least how can I find information on how to add these
> parameters properly?
>
> Anna
>
>
> __
> Anna Marabotti,
> Ph.D.
> Assistant Professor
> Department of Chemistry and Biology
> University
> of Salerno
> Via Ponte don Melillo
> 84084 Fisciano (SA)
> Italy
> Phone: +39
> 089 969583
> Fax: +39 089 969603
> E-mail: amarabo...@unisa.it
> Skype:
> annam1972
>
> "When a man with a gun meets a man with a pen, the man with
> the gun is a dead man"
> (Roberto Benigni, about Roberto Saviano)
>  Il
> 21/03/2013 21:53, gmx-users-requ...@gromacs.org [1] ha scritto:
>
>
>
>
> Links:
> --
> [1] mailto:gmx-users-requ...@gromacs.org
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
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Re: [gmx-users] Error in REMD

[Mark Abraham]

This would normally mean you are somehow calling code from one GROMACS
version with code from another. Some kind of dynamic library loading mishap?

Mark

On Fri, Mar 22, 2013 at 10:41 AM, Nikunj Maheshwari <
nixcrazyfor...@gmail.com> wrote:

> Dear all...
>
> We ran REMD simulations for 36 replicas. We got an error which stopped the
> whole simulation.
>
> "
> Reading file md21.tpr, VERSION 4.5.5 (single precision)
> Loaded with Money
>
> Reading file md24.tpr, VERSION 4.5.5 (single precision)
> Loaded with Money
>
>
> ---
> Program mdrun_mpi, VERSION 4.5.5
> Source code file: symtab.c, line: 108
>
> Fatal error:
> symtab get_symtab_handle 1031126655 not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> "The World is a Friendly Place" (Magnapop)
>
> Error on node 35, will try to stop all the nodes
> Halting parallel program mdrun_mpi on CPU 35 out of 36
>
> gcq#103: "The World is a Friendly Place" (Magnapop)
>
> MPI: Global rank 35 is aborting with error code -1.
> "
>
> Can someone help us in knowing what the error means and how to it can be
> rectified?
>
> Thanks
> --
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Re: [gmx-users] how can we obtain replicated trajectory?

[Mark Abraham]

As you can see in your plot, no replicas from 400K got down to 300K in the
1.5ns you simulated. So you've so far derived no benefit from REMD (unless
you want sampling at lots of temperatures). Perhaps a simulation a hundred
times longer might get a few such events? You might as well have run a
simulation at 400K to see what it did... What do you hope REMD will help
you observe?

Mark

On Fri, Mar 22, 2013 at 12:28 PM, Albert  wrote:

> Hello:
>
>  I've finished a replica exchange simulation with 72 replica (300K-580K)
> under explicit solvent model. It generate 72 trajectory and the replica
> since to "cross" well with neighboring temperature. Here is the figure:
>
>
> http://dl.dropbox.com/u/**56271062/REMD.png
>
>  I am just wondering how can we generate and visualize the system at 300 K
>  with that at 400-500 K? There is a ligand in my system, and it is expected
> to escape binding pocket with large loop movement
>
> thank you very much
>
> best
> Albert
> --
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Re: [gmx-users] how can we obtain replicated trajectory?

[Albert]

On 03/22/2013 03:45 PM, Mark Abraham wrote:

As you can see in your plot, no replicas from 400K got down to 300K in the
1.5ns you simulated. So you've so far derived no benefit from REMD (unless
you want sampling at lots of temperatures). Perhaps a simulation a hundred
times longer might get a few such events? You might as well have run a
simulation at 400K to see what it did... What do you hope REMD will help
you observe?

Mark



HI Mark

 thanks a lot for such kind advices and comments.

 There is a ligand in my protein binding site and I hope REMD can 
enable me how the ligand escape binding pocket coupled with some big 
loop movement.


thank you very much.

best
Albert
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Re: [gmx-users] Hydrogen bonding differences

[Kavyashree M]

Dear Users,

As suggested earlier by Erik I used 4.6 to calculate the hydrogen bonds.
Still the
Total intra-protein hydrogen bonds is not equal (MM +MS +SS) hydrogen bond.
Is there any other solution?

Thank you
Kavya

On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M  wrote:

> Dear Sir,
>
> Sure I will try with 4.6. presently I am not able to download it.
>
> Thank you
> kavya
>
>
> On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund wrote:
>
>> There were a handful of bugfixes to g_hbond over the last year. Could you
>> try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form before.
>>
>> Erik
>>
>>
>> On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote:
>>
>>  Dear Sir,
>>>
>>> This is 4.5.3. I have not tried nomerge. I did not use
>>> nomerge option in any of them, So if it has counted
>>> it (Hbond b/w same donor and acceptor but with
>>> different hydrogen) twice in one calculation then it will
>>> be counted twice in another, So wont the result with/without
>>> nomerge be the same?
>>>
>>> The difference is 4-5 Hbonds..
>>>
>>> Thank you
>>> Kavya
>>>
>>> On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund 
>>> wrote:
>>>
>>>  Hi. What version was this? Have you tried with -nomerge?

 Erik


 On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote:

 Dear users,

>
> While calculating hydrogen bonds for a simulation, it
> was found that the average number of intra protein
> hbonds was not equal to sum of MM, MS and SS
> hydrogen bonds. (MM - main chain - main chain,
> MS - main chain - side chain and side chain - side
> chain hydrogen bonds). There was a difference of 5
> or so hbonds between intra-protein and MM+MS+SS
> hbonds. why is this so?
> I selected the options 7 7 for MM, 7 8 for MS and 8 8
> for SS hydrogen bonds.
>
> One clarification. nhbdist option gives 0, 1, 2, 3 and
> total hydrogen bonds per hydrogen. Does this mean
> that a single hydrogen involving in forming hbond with
> 2 different acceptors/donors at different points of time
> in the trajectory.
>
> Thanks
> kavya
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Re: [gmx-users] Hydrogen bonding differences

[Erik Marklund]

I could see how -merge (on by default) could lead to this. Have you  
tried -nomerge?


Erik

On Mar 22, 2013, at 4:46 PM, Kavyashree M wrote:


Dear Users,

As suggested earlier by Erik I used 4.6 to calculate the hydrogen  
bonds.

Still the
Total intra-protein hydrogen bonds is not equal (MM +MS +SS)  
hydrogen bond.

Is there any other solution?

Thank you
Kavya

On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M   
wrote:



Dear Sir,

Sure I will try with 4.6. presently I am not able to download it.

Thank you
kavya


On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund  
wrote:


There were a handful of bugfixes to g_hbond over the last year.  
Could you
try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form  
before.


Erik


On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote:

Dear Sir,


This is 4.5.3. I have not tried nomerge. I did not use
nomerge option in any of them, So if it has counted
it (Hbond b/w same donor and acceptor but with
different hydrogen) twice in one calculation then it will
be counted twice in another, So wont the result with/without
nomerge be the same?

The difference is 4-5 Hbonds..

Thank you
Kavya

On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund >

wrote:

Hi. What version was this? Have you tried with -nomerge?


Erik


On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote:

Dear users,



While calculating hydrogen bonds for a simulation, it
was found that the average number of intra protein
hbonds was not equal to sum of MM, MS and SS
hydrogen bonds. (MM - main chain - main chain,
MS - main chain - side chain and side chain - side
chain hydrogen bonds). There was a difference of 5
or so hbonds between intra-protein and MM+MS+SS
hbonds. why is this so?
I selected the options 7 7 for MM, 7 8 for MS and 8 8
for SS hydrogen bonds.

One clarification. nhbdist option gives 0, 1, 2, 3 and
total hydrogen bonds per hydrogen. Does this mean
that a single hydrogen involving in forming hbond with
2 different acceptors/donors at different points of time
in the trajectory.

Thanks
kavya
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Re: [gmx-users] proper and improper dihedrals in topology file from other ff

[Justin Lemkul]

On 3/22/13 9:18 AM, 라지브간디 wrote:

Dear Justin,


I got understand the gromos ff improper style. however, what i am asking here 
is how would i use the charmm/amber improper from literuatre where they 
indicate the improper in this was ( something X-X)




Improper

CPB-X-X-CR1E 90.0 0.0
CC - X-X-NB 18.3 0.0








What X shows here and how do i use this in gromos format way?




I don't understand entirely what you're trying to do.  You shouldn't be trying 
to implement CHARMM or AMBER parameters in Gromos.  X is a generic indicator 
signifying any atom.


-Justin

--


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


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Re: [gmx-users] Hydrogen bonding differences

[Kavyashree M]

Sir,

I tried -nomerge. It is fine now. But will it be wrong to
calculate without nomerge option?

Thank you
Kavya

On Fri, Mar 22, 2013 at 9:28 PM, Erik Marklund  wrote:

> I could see how -merge (on by default) could lead to this. Have you tried
> -nomerge?
>
> Erik
>
>
> On Mar 22, 2013, at 4:46 PM, Kavyashree M wrote:
>
>  Dear Users,
>>
>> As suggested earlier by Erik I used 4.6 to calculate the hydrogen bonds.
>> Still the
>> Total intra-protein hydrogen bonds is not equal (MM +MS +SS) hydrogen
>> bond.
>> Is there any other solution?
>>
>> Thank you
>> Kavya
>>
>> On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M  wrote:
>>
>>  Dear Sir,
>>>
>>> Sure I will try with 4.6. presently I am not able to download it.
>>>
>>> Thank you
>>> kavya
>>>
>>>
>>> On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund >> >wrote:
>>>
>>>  There were a handful of bugfixes to g_hbond over the last year. Could
 you
 try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form
 before.

 Erik


 On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote:

 Dear Sir,

>
> This is 4.5.3. I have not tried nomerge. I did not use
> nomerge option in any of them, So if it has counted
> it (Hbond b/w same donor and acceptor but with
> different hydrogen) twice in one calculation then it will
> be counted twice in another, So wont the result with/without
> nomerge be the same?
>
> The difference is 4-5 Hbonds..
>
> Thank you
> Kavya
>
> On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund 
> wrote:
>
> Hi. What version was this? Have you tried with -nomerge?
>
>>
>> Erik
>>
>>
>> On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote:
>>
>> Dear users,
>>
>>
>>> While calculating hydrogen bonds for a simulation, it
>>> was found that the average number of intra protein
>>> hbonds was not equal to sum of MM, MS and SS
>>> hydrogen bonds. (MM - main chain - main chain,
>>> MS - main chain - side chain and side chain - side
>>> chain hydrogen bonds). There was a difference of 5
>>> or so hbonds between intra-protein and MM+MS+SS
>>> hbonds. why is this so?
>>> I selected the options 7 7 for MM, 7 8 for MS and 8 8
>>> for SS hydrogen bonds.
>>>
>>> One clarification. nhbdist option gives 0, 1, 2, 3 and
>>> total hydrogen bonds per hydrogen. Does this mean
>>> that a single hydrogen involving in forming hbond with
>>> 2 different acceptors/donors at different points of time
>>> in the trajectory.
>>>
>>> Thanks
>>> kavya
>>> -- gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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>>> posting!
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Re: [gmx-users] how can we obtain replicated trajectory?

[Mark Abraham]

On Fri, Mar 22, 2013 at 3:54 PM, Albert  wrote:

> On 03/22/2013 03:45 PM, Mark Abraham wrote:
>
>> As you can see in your plot, no replicas from 400K got down to 300K in the
>> 1.5ns you simulated. So you've so far derived no benefit from REMD (unless
>> you want sampling at lots of temperatures). Perhaps a simulation a hundred
>> times longer might get a few such events? You might as well have run a
>> simulation at 400K to see what it did... What do you hope REMD will help
>> you observe?
>>
>> Mark
>>
>
>
> HI Mark
>
>  thanks a lot for such kind advices and comments.
>
>  There is a ligand in my protein binding site and I hope REMD can enable
> me how the ligand escape binding pocket coupled with some big loop movement.
>

"How" implies you need to see the process by which such an event occurs,
which you can't do in REMD because if the trajectory is continuous then its
ensemble was not, and vice versa. If your REMD sampling is exhaustive, then
you may "catch" some frames around 300K in the process of escaping, but
probably you can't afford that much computer time. Using a pulling
simulation to force the reaction coordinate to sample the space that
interests you is likely a much more productive way to enhance your
sampling. Check the literature!

Mark
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Re: [gmx-users] Hydrogen bonding differences

[Erik Marklund]

I wouldn't say wrong, but I realized that some residue may make two  
hbonds to different parts of the protein, i.e. to the main chain and  
to a side chain at the same time. With -merge this counts as one if  
you analyze the entire protein. If you split your analysis such hbonds  
will show up in both e.g. SS and MS, hence TOT < MM+SS+MS. It's just  
another way of counting hbonds.


Erik

On Mar 22, 2013, at 5:32 PM, Kavyashree M wrote:


Sir,

I tried -nomerge. It is fine now. But will it be wrong to
calculate without nomerge option?

Thank you
Kavya

On Fri, Mar 22, 2013 at 9:28 PM, Erik Marklund  
 wrote:


I could see how -merge (on by default) could lead to this. Have you  
tried

-nomerge?

Erik


On Mar 22, 2013, at 4:46 PM, Kavyashree M wrote:

Dear Users,


As suggested earlier by Erik I used 4.6 to calculate the hydrogen  
bonds.

Still the
Total intra-protein hydrogen bonds is not equal (MM +MS +SS)  
hydrogen

bond.
Is there any other solution?

Thank you
Kavya

On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M   
wrote:


Dear Sir,


Sure I will try with 4.6. presently I am not able to download it.

Thank you
kavya


On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund  

wrote:


There were a handful of bugfixes to g_hbond over the last year.  
Could

you
try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form
before.

Erik


On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote:

Dear Sir,



This is 4.5.3. I have not tried nomerge. I did not use
nomerge option in any of them, So if it has counted
it (Hbond b/w same donor and acceptor but with
different hydrogen) twice in one calculation then it will
be counted twice in another, So wont the result with/without
nomerge be the same?

The difference is 4-5 Hbonds..

Thank you
Kavya

On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund >

wrote:

Hi. What version was this? Have you tried with -nomerge?



Erik


On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote:

Dear users,



While calculating hydrogen bonds for a simulation, it
was found that the average number of intra protein
hbonds was not equal to sum of MM, MS and SS
hydrogen bonds. (MM - main chain - main chain,
MS - main chain - side chain and side chain - side
chain hydrogen bonds). There was a difference of 5
or so hbonds between intra-protein and MM+MS+SS
hbonds. why is this so?
I selected the options 7 7 for MM, 7 8 for MS and 8 8
for SS hydrogen bonds.

One clarification. nhbdist option gives 0, 1, 2, 3 and
total hydrogen bonds per hydrogen. Does this mean
that a single hydrogen involving in forming hbond with
2 different acceptors/donors at different points of time
in the trajectory.

Thanks
kavya
-- gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/**mailman/listinfo/gmx-users
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Re: [gmx-users] Mismatching number of PP MPI processes and GPUs per node

[Szilárd Páll]

Hi,

Actually, if you don't want to run across the network, with those Westmere
processors you should be fine with running OpenMP across the two sockets,
i.e
mdrun -ntomp 24
or to run without HyperThreading (which can be sometimes faster) just use
mdrun -ntomp 12 -pin on

Now, when it comes to GPU runs, your CPUs are so much faster than that
rather slow Quadro card, that I doubt you will see any benefit from using
it, but you should try.

One other thing to consider is and even more complicated way of doing work
sharing between CPU and GPU, but for this you need domain decomposition,
hence MPI, hence multiple ranks per GPU, hence thread-MPI won't work:
mpirun -np 2 mdrun_mpi -ntomp 6 -gpu_id 00 -nb gpu_cpu
(that is without HT).

Cheers,


--
Szilárd


On Fri, Mar 22, 2013 at 3:20 AM, George Patargias wrote:

> Hello Szilard
>
> Many thanks for these very useful comments!
>
> We run jobs on a single node of a small Apple cluster (no Infiniband
> unfortunately). One node has two Intel(R) Xeon(R) X5650 Processors each
> with 6 cores and 12 threads, so in total 12 cores and 24 threads.
>
> I have compiled GROMACS 4.6.1 with OpenMP and CUDA support (-DGMX_MPI=OFF)
>
> Do I understand correctly that this build will work efficiently without gpu
> but not with gpu as you mention?
>
> In order to run gromacs according to your suggestion
>
> mpirun -np 2 -ntomp 6 mdrun_mpi -s test.tpr -deffnm test_out -gpu_id 00
>
> Do I need to compile with MPI (i.e. -DGMX_MPI=ON)?
>
> Would this then be the most efficient way to run GROMACS in the given
> hardware set-up (dual socket, total 12 cores and GPU)?
>
> Thanks again!
>
> Best
> George
>
>
>
>
> > FYI: On your machine running OpenMP across two sockets will probably not
> be
> > very efficient. Depending on the input and at how high paralleliation
> are
> > you running, you could be better off with running multiple MPI ranks per
> GPU. This is a bit of an unexplained feature due to it being complicated
> to
> > use and not fully supported (does not woth with thread-MPI), but you can
> essentially make  multiple MPI ranks use the same GPU by passing the ID
> of
> > the GPU you want to "overload" multiple times (and launching the correct
> number of MPI ranks).
> > For instance, in your case you can try putting one MPI rank per socket,
> both using GPU 0 by:
> > mpirun -np 2 -ntomp 6 mdrun_mpi -s test.tpr -deffnm test_out -nb gpu
> -gpu_id 00
> > This is briefly explained on the wiki as well:
> >
> http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multiple_MPI_ranks_per_GPU
> Let us know whether you are able to get useful speedup from GPUs!
> Cheers,
> > --
> > Szil?rd
> > On Tue, Mar 12, 2013 at 10:06 AM, George Patargias
> > wrote:
> >> Hi Carsten
> >> Thanks a lot for this tip. It worked!
> >> George
> >> > Hi,
> >> > On Mar 11, 2013, at 10:50 AM, George Patargias 
> >> wrote:
> >> >> Hello
> >> >> Sorry for posting this again.
> >> >> I am trying to run GROMACS 4.6 compiled with MPI and GPU
> acceleration
> >> >> (CUDA 5.0 lib) using the following SGE batch script.
> >> >> #!/bin/sh
> >> >> #$ -V
> >> >> #$ -S /bin/sh
> >> >> #$ -N test-gpus
> >> >> #$ -l h="xgrid-node02"
> >> >> #$ -pe mpi_fill_up 12
> >> >> #$ -cwd
> >> >> source /opt/NetUsers/pgkeka/gromacs-4.6_gpu_mpi/bin/GMXRC
> >> >> export
> >> >> DYLD_LIBRARY_PATH=/Developer/NVIDIA/CUDA-5.0/lib:$DYLD_LIBRARY_PATH
> mpirun -np 12 mdrun_mpi -s test.tpr -deffnm test_out -nb gpu After
> detection of the installed GPU card
> >> >> 1 GPU detected on host xgrid-node02.xgrid:
> >> >>  #0: NVIDIA Quadro 4000, compute cap.: 2.0, ECC:  no, stat:
> >> compatible
> >> >> GROMACS issues the following error
> >> >> Incorrect launch configuration: mismatching number of PP MPI
> >> processes
> >> >> and
> >> >> GPUs per node. mdrun_mpi was started with 12 PP MPI processes per
> >> node,
> >> >> but only 1 GPU were detected.
> >> >> It can't be that we need to run GROMACS only on a single core so
> that
> >> it
> >> >> matches the single GPU card.
> >> > Have you compiled mdrun_mpi with OpenMP threads support? Then, if you
> do
> >> > mpirun -np 1 mdrun_mpi ?
> >> > it should start one MPI process with 12 OpenMP threads, which should
> >> give
> >> > you what you want. You can also manually specify the number of OpenMP
> threads
> >> > by adding
> >> > -ntomp 12
> >> > Carsten
> >> >> Do you have any idea what has to be done?
> >> >> Many thanks.
> >> >> Dr. George Patargias
> >> >> Postdoctoral Researcher
> >> >> Biomedical Research Foundation
> >> >> Academy of Athens
> >> >> 4, Soranou Ephessiou
> >> >> 115 27
> >> >> Athens
> >> >> Greece
> >> >> Office: +302106597568
> >> >> --
> >> >> gmx-users mailing listgmx-users@gromacs.org
> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> interface or send it to gmx-use

[gmx-users] Proper and improper from other ff?

[라지브간디]

Dear Justin,

Actually I've manually added the heme -ligand parameters details such as bond, 
angle and dihedral to my topology created by pdb2gmx via gromos43a1. ( Those 
manually added parameters details are taken from charmm and amber ff, which are 
available in some published articles ). 
I confused while interpreting the improper values from those published article 
where they both shown (amber and charmm) improper in X (generic indicator) way, 
whereas the gromos improper values for atoms are in direct way by not using X 
generic indicator. 

Is that improper details are important for heme-ligand case ? If so, how do I 
make them favor to gromos by this article values ?

Thanks in advance 




I don't understand entirely what you're trying to do. You shouldn't be trying 
to implement CHARMM or AMBER parameters in Gromos. X is a generic indicator 
signifying atoms 
Justin.

> I got understand the gromos ff improper style. however, what i am asking here 
> is how would i use the charmm/amber improper from literuatre where they 
> indicate the improper in this was ( something X-X) 
> 
> 
> 
> 
> Improper 
>> CPB-X-X-CR1E 90.0 0.0 
>> CC - X-X-NB 18.3 0.0 
>> 
> 
> 
> 
> 
> 
> 
> What X shows here and how do i use this in gromos format way? 
> 
> 

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Re: [gmx-users] Proper and improper from other ff?

[Justin Lemkul]

On 3/22/13 3:14 PM, 라지브간디 wrote:


Dear Justin,

Actually I've manually added the heme -ligand parameters details such as bond, 
angle and dihedral to my topology created by pdb2gmx via gromos43a1. ( Those 
manually added parameters details are taken from charmm and amber ff, which are 
available in some published articles ).


If you're doing this, you're creating a hybrid force field that makes no sense. 
 There are parameters for heme within Gromos96 already; why are you making 
these modifications?



I confused while interpreting the improper values from those published article 
where they both shown (amber and charmm) improper in X (generic indicator) way, 
whereas the gromos improper values for atoms are in direct way by not using X 
generic indicator.

Is that improper details are important for heme-ligand case ? If so, how do I 
make them favor to gromos by this article values ?



Different force fields derive and implement parameters in different ways.  Hence 
why it makes no sense to try to combine them.


-Justin

--


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


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Re: [gmx-users] Hydrogen bonding differences

[Kavyashree M]

Thank you Sir for clarifying the confusion.

Regards
kavya

On Fri, Mar 22, 2013 at 11:18 PM, Erik Marklund wrote:

> I wouldn't say wrong, but I realized that some residue may make two hbonds
> to different parts of the protein, i.e. to the main chain and to a side
> chain at the same time. With -merge this counts as one if you analyze the
> entire protein. If you split your analysis such hbonds will show up in both
> e.g. SS and MS, hence TOT < MM+SS+MS. It's just another way of counting
> hbonds.
>
> Erik
>
>
> On Mar 22, 2013, at 5:32 PM, Kavyashree M wrote:
>
>  Sir,
>>
>> I tried -nomerge. It is fine now. But will it be wrong to
>> calculate without nomerge option?
>>
>> Thank you
>> Kavya
>>
>> On Fri, Mar 22, 2013 at 9:28 PM, Erik Marklund 
>> wrote:
>>
>>  I could see how -merge (on by default) could lead to this. Have you tried
>>> -nomerge?
>>>
>>> Erik
>>>
>>>
>>> On Mar 22, 2013, at 4:46 PM, Kavyashree M wrote:
>>>
>>> Dear Users,
>>>

 As suggested earlier by Erik I used 4.6 to calculate the hydrogen bonds.
 Still the
 Total intra-protein hydrogen bonds is not equal (MM +MS +SS) hydrogen
 bond.
 Is there any other solution?

 Thank you
 Kavya

 On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M 
 wrote:

 Dear Sir,

>
> Sure I will try with 4.6. presently I am not able to download it.
>
> Thank you
> kavya
>
>
> On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund 
>> wrote:
>>
>
> There were a handful of bugfixes to g_hbond over the last year. Could
>
>> you
>> try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form
>> before.
>>
>> Erik
>>
>>
>> On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote:
>>
>> Dear Sir,
>>
>>
>>> This is 4.5.3. I have not tried nomerge. I did not use
>>> nomerge option in any of them, So if it has counted
>>> it (Hbond b/w same donor and acceptor but with
>>> different hydrogen) twice in one calculation then it will
>>> be counted twice in another, So wont the result with/without
>>> nomerge be the same?
>>>
>>> The difference is 4-5 Hbonds..
>>>
>>> Thank you
>>> Kavya
>>>
>>> On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund >> >
>>> wrote:
>>>
>>> Hi. What version was this? Have you tried with -nomerge?
>>>
>>>
 Erik


 On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote:

 Dear users,


  While calculating hydrogen bonds for a simulation, it
> was found that the average number of intra protein
> hbonds was not equal to sum of MM, MS and SS
> hydrogen bonds. (MM - main chain - main chain,
> MS - main chain - side chain and side chain - side
> chain hydrogen bonds). There was a difference of 5
> or so hbonds between intra-protein and MM+MS+SS
> hbonds. why is this so?
> I selected the options 7 7 for MM, 7 8 for MS and 8 8
> for SS hydrogen bonds.
>
> One clarification. nhbdist option gives 0, 1, 2, 3 and
> total hydrogen bonds per hydrogen. Does this mean
> that a single hydrogen involving in forming hbond with
> 2 different acceptors/donors at different points of time
> in the trajectory.
>
> Thanks
> kavya
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