date:20180312


Hi all,

There seems to be a problem with the new pull code when it comes to 
using it for umbrella sampling with 'distance' directive for WHAM (the 
original thread is my earlier exchange with Justin in '[gmx-users] 
seeming paradox with gmx wham'). In order to subdue unknown statement 
errors, the code was modified to:


pull = yes
pull-coord1-type = umbrella
pull_ngroups    = 2
pull_ncoords    = 1
pull_group1_name    = K
pull_group2_name    = CNT
pull_coord1_geometry    = distance
pull_coord1_groups  = 1 2
pull-coord1-dim = Y Y Y
pull_coord1_rate    = 0.0
pull_coord1_k   = 1000
pull_coord1_start   = yes

But it is a mess anyway. The box is 5.7 nm tall (6 nm by 5.5 nm wide) 
and the membrane's COM is definitely close to the geometric center of 
the box and it is definitely not moving beyond a few angstroms from 
thermal fluctuations (the membrane is very strongly restrained at its 
perimeter). The initial coordinate configurations for the other group 
(an ion) are a sweep of heights between -1.5 nm and 1.5 nm right 
relative to the membrane's COM along the height -- initial x and y are 
those of the membrane's COM -- see my very angry drawing here: 
https://www.dropbox.com/s/bwugqp5v9qt7iaq/pull.jpg?dl=0   :) The 
distance simply cannot exceed 1.5 nm with spherical symmetry, it just 
can't. And yet, i get errors like


"Distance between pull groups 1 and 2 (3.035939 nm) is larger than 0.49 
times the box size (2.728418)." -- this is from grompp


Sometimes grompp is actually satisfied, but then mdrun throws this after 
a few thousand steps:


"Program: gmx mdrun, version 2018
Source file: src/gromacs/pulling/pull.cpp (line 707)
MPI rank:    0 (out of 2)

Fatal error:
Distance between pull groups 1 and 2 (2.732163 nm) is larger than 0.49 times
the box size (2.728418)."

This does not seem possible, because at this point the ion is radially 
restrained (1000 kJ/mol/nm2). This was /never/ an issue with 5.0.4 with 
a considerably smaller box (4 nm) -- the entire mdp file is a copy of 
what worked in 5.0.4, except the pull code is as above. Do I just 
continue increasing the box size?


Thanks,

Alex

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[gmx-users] Error while Installing GROMACS 2018 on Dell EMC T640(Xeon Gold 6152) with Tesla K880 GPU (RHEL 7.3)

2018-03-12 Thread 신동규

I am trying to install the latest GROMACS on Dell EMC T640(Xeon Gold
6152) with Tesla K880 GPU (RHEL 7.3) but got the following error when
issuing cmake command.

My command was:

cmake ..  -DGMX_GPU=on -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

I  tried with option -DGMX_SIMD=AVX_512 but the result was same.

Thanks in advance for the help.




[root@xxx build]# cmake ..  -DGMX_GPU=on -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON





-- Detecting best SIMD instructions for this CPU

-- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED
-- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed
-- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED
-- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED - Failed
-- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED
-- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED - Failed
-- Performing Test C_mavx512f_FLAG_ACCEPTED
-- Performing Test C_mavx512f_FLAG_ACCEPTED - Failed
-- Performing Test C_arch_AVX_FLAG_ACCEPTED
-- Performing Test C_arch_AVX_FLAG_ACCEPTED - Failed
-- Performing Test C_hgnu_FLAG_ACCEPTED
-- Performing Test C_hgnu_FLAG_ACCEPTED - Failed
-- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS
-- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed
-- Could not find any flag to build test source (this could be due to
either the compiler or binutils)
-- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED
-- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed
-- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED
-- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED - Failed
-- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED
-- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED - Failed
-- Performing Test CXX_mavx512f_FLAG_ACCEPTED
-- Performing Test CXX_mavx512f_FLAG_ACCEPTED - Failed
-- Performing Test CXX_arch_AVX_FLAG_ACCEPTED
-- Performing Test CXX_arch_AVX_FLAG_ACCEPTED - Failed
-- Performing Test CXX_hgnu_FLAG_ACCEPTED
-- Performing Test CXX_hgnu_FLAG_ACCEPTED - Failed
-- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS
-- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed
-- Could not find any flag to build test source (this could be due to
either the compiler or binutils)
-- Could not identify number of AVX-512 units - detection program
missing compilation prerequisites
-- Could not run code to detect number of AVX-512 FMA units - assuming 2.
-- Detected best SIMD instructions for this CPU - AVX_512
CMake Error at cmake/gmxManageSimd.cmake:51 (message):
  Cannot find AVX 512F compiler flag.  Use a newer compiler, or choose a
  lower level of SIMD (slower).
Call Stack (most recent call first):
  cmake/gmxManageSimd.cmake:186
(gmx_give_fatal_error_when_simd_support_not_found)
  CMakeLists.txt:703 (gmx_manage_simd)
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Re: [gmx-users] seeming paradox with gmx wham

You actually pointed this symmetry situation out when I was calculating
something that's already been submitted, so the gratitude is all mine.
Hopefully, it doesn't produce much of a difference in that particular case,
but I really should have listened. The path to correcting possible
artifacts is clear. :)

Alex

On Mon, Mar 12, 2018 at 5:03 PM, Justin Lemkul  wrote:

>
>
> On 3/12/18 6:59 PM, Alex wrote:
>
>> Great, thanks. I believe this necessitates an acknowledgment. You go by J.
>> A. Lemkul in your papers, correct?
>>
> That would work. Much obliged :)
>
> -Justin
>
>
> On Mon, Mar 12, 2018 at 4:56 PM, Justin Lemkul  wrote:
>>
>> r
>>>
>>> On 3/12/18 6:54 PM, Alex wrote:
>>>
>>> Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point, it's
 still a small system. My sampling pull code is below, I only modified
 the
 bare minimum to work with the new pull code syntax and to enable
 spherical
 slices (radius varying from near-zero to 1.5 nm):

 pull = yes
 pull-coord1-type = umbrella
 pull_ngroups= 2
 pull_ncoords= 1
 pull_group1_name= CL
 pull_group2_name= CNT
 pull_coord1_geometry= distance
 pull_coord1_groups  = 1 2
 pull_dim= Y Y Y
 pull_coord1_rate= 0.0
 pull_coord1_k   = 1000
 pull_start  = yes

 CNT is the colloquial name for our membrane. I'm trying to be
 extra-careful
 this time, so I will really appreciate if you see anything else that
 looks
 wrong. Another quick question: it is my understanding that the value of
 k
 will control the histogram width. Is 1000 a reasonable choice overall?

 No way to know. It depends on the window spacing and the forces acting
>>> in
>>> the system. I don't know that anyone has come up with a way to actually
>>> know what's "right" for umbrella sampling other than empirical
>>> assignment.
>>>
>>> Everything else looks reasonable to me.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
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Re: [gmx-users] seeming paradox with gmx wham




On 3/12/18 6:59 PM, Alex wrote:

Great, thanks. I believe this necessitates an acknowledgment. You go by J.
A. Lemkul in your papers, correct?

That would work. Much obliged :)

-Justin


On Mon, Mar 12, 2018 at 4:56 PM, Justin Lemkul  wrote:


r

On 3/12/18 6:54 PM, Alex wrote:


Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point, it's
still a small system. My sampling pull code is below, I only modified the
bare minimum to work with the new pull code syntax and to enable spherical
slices (radius varying from near-zero to 1.5 nm):

pull = yes
pull-coord1-type = umbrella
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= CL
pull_group2_name= CNT
pull_coord1_geometry= distance
pull_coord1_groups  = 1 2
pull_dim= Y Y Y
pull_coord1_rate= 0.0
pull_coord1_k   = 1000
pull_start  = yes

CNT is the colloquial name for our membrane. I'm trying to be
extra-careful
this time, so I will really appreciate if you see anything else that looks
wrong. Another quick question: it is my understanding that the value of k
will control the histogram width. Is 1000 a reasonable choice overall?


No way to know. It depends on the window spacing and the forces acting in
the system. I don't know that anyone has come up with a way to actually
know what's "right" for umbrella sampling other than empirical assignment.

Everything else looks reasonable to me.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] seeming paradox with gmx wham

Great, thanks. I believe this necessitates an acknowledgment. You go by J.
A. Lemkul in your papers, correct?

On Mon, Mar 12, 2018 at 4:56 PM, Justin Lemkul  wrote:

> r
>
> On 3/12/18 6:54 PM, Alex wrote:
>
>> Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point, it's
>> still a small system. My sampling pull code is below, I only modified the
>> bare minimum to work with the new pull code syntax and to enable spherical
>> slices (radius varying from near-zero to 1.5 nm):
>>
>> pull = yes
>> pull-coord1-type = umbrella
>> pull_ngroups= 2
>> pull_ncoords= 1
>> pull_group1_name= CL
>> pull_group2_name= CNT
>> pull_coord1_geometry= distance
>> pull_coord1_groups  = 1 2
>> pull_dim= Y Y Y
>> pull_coord1_rate= 0.0
>> pull_coord1_k   = 1000
>> pull_start  = yes
>>
>> CNT is the colloquial name for our membrane. I'm trying to be
>> extra-careful
>> this time, so I will really appreciate if you see anything else that looks
>> wrong. Another quick question: it is my understanding that the value of k
>> will control the histogram width. Is 1000 a reasonable choice overall?
>>
>
> No way to know. It depends on the window spacing and the forces acting in
> the system. I don't know that anyone has come up with a way to actually
> know what's "right" for umbrella sampling other than empirical assignment.
>
> Everything else looks reasonable to me.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] seeming paradox with gmx wham


r

On 3/12/18 6:54 PM, Alex wrote:

Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point, it's
still a small system. My sampling pull code is below, I only modified the
bare minimum to work with the new pull code syntax and to enable spherical
slices (radius varying from near-zero to 1.5 nm):

pull = yes
pull-coord1-type = umbrella
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= CL
pull_group2_name= CNT
pull_coord1_geometry= distance
pull_coord1_groups  = 1 2
pull_dim= Y Y Y
pull_coord1_rate= 0.0
pull_coord1_k   = 1000
pull_start  = yes

CNT is the colloquial name for our membrane. I'm trying to be extra-careful
this time, so I will really appreciate if you see anything else that looks
wrong. Another quick question: it is my understanding that the value of k
will control the histogram width. Is 1000 a reasonable choice overall?


No way to know. It depends on the window spacing and the forces acting 
in the system. I don't know that anyone has come up with a way to 
actually know what's "right" for umbrella sampling other than empirical 
assignment.


Everything else looks reasonable to me.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] seeming paradox with gmx wham

Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point, it's
still a small system. My sampling pull code is below, I only modified the
bare minimum to work with the new pull code syntax and to enable spherical
slices (radius varying from near-zero to 1.5 nm):

pull = yes
pull-coord1-type = umbrella
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= CL
pull_group2_name= CNT
pull_coord1_geometry= distance
pull_coord1_groups  = 1 2
pull_dim= Y Y Y
pull_coord1_rate= 0.0
pull_coord1_k   = 1000
pull_start  = yes

CNT is the colloquial name for our membrane. I'm trying to be extra-careful
this time, so I will really appreciate if you see anything else that looks
wrong. Another quick question: it is my understanding that the value of k
will control the histogram width. Is 1000 a reasonable choice overall?

Thank you,

Alex

On Mon, Mar 12, 2018 at 4:07 PM, Justin Lemkul  wrote:

>
>
> On 3/12/18 3:42 PM, Alex wrote:
>
>> I actually understood your tutorial perfectly well. What I didn't expect
>> is such a significant dependence on direction (assuming spherical symmetry
>> clears the situation).
>>
>> I also had to use direction-periodic instead of distance in your
>> tutorial, because the box is 4 nm wide and grompp is screaming about
>> distance exceeding half-box size. I used 5.0.3 before and it was fine with
>> the 'distance' directive. I think 'direction-periodic' is also wrong for
>> spherical symmetry. So, stick with distance and increase box size?
>>
>> That's the easiest thing to do, yes, as long as the simulation is still
> reasonably efficient.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Regarding minimum size

Hi,

That's not a valid way to use these components. Whatever you're trying to
do shouldn't be attempted by trying to call mdrunner.mainFunction() twice.

Mark

On Mon, Mar 12, 2018 at 9:54 PM Chhavi Yadav  wrote:

> I wrote this code and was running the debugger:
>
>
> int main(int argc, char *argv[]) {
>
>
> int rc;
> MD mdrunner;
> rc = mdrunner.mainFunction(argc, argv);
> printf("Potential Energy from integrator: %.6f\n", mdrunner.epot);
>
> mdrunner.epot = 0;
>
> t_state *t = mdrunner.globalState.get();
> t->x[0][0] = 10.0;
> t->x[0][1] = 10.0;
> t->x[0][2] = 10.0;
>
>
> rc = mdrunner.mainFunction(argc, argv);
> printf("Potential Energy from integrator: %.6f\n", mdrunner.epot);
>
> return rc;
>
> }
>
> OUTPUT:
>
> Reading file 1aki/1AKI.tpr, VERSION
> 2018-dev-20180223-a989b355c-dirty-unknown (single precision)
>
> NOTE: disabling dynamic load balancing as it is not supported in reruns.
>
> No option -multi
> No option -multi
> No option -multi
> No option -multi
> No option -multi
> No option -multi
> No option -multi
> No option -multi
> Using 8 MPI threads
> starting md rerun 'LYSOZYME', reading coordinates from input trajectory
> '1aki/1AKI.gro'
>
> Reading frames from gro file 'LYSOZYME;', 1960 atoms.
>
> Reading frame   0 time0.000
> WARNING: Some frames do not contain velocities.
>  Ekin, temperature and pressure are incorrect,
>  the virial will be incorrect when constraints are present.
>
>
> Last frame  0 time0.000
>
>Core t (s)   Wall t (s)(%)
>Time:0.9610.120  800.0
>  (ns/day)(hour/ns)
> Performance:0.719   33.377
> Potential Energy from integrator: -8519.961914
>
> NOTE: disabling dynamic load balancing as it is not supported in reruns.
>
>
> ---
> Program: GROMACS, version 2018-dev-20180308-65a7ab86c-dirty-unknown
> Source file: src/gromacs/domdec/domdec.cpp (line 6571)
> MPI rank:0 (out of 8)
>
> Fatal error:
> There is no domain decomposition for 8 ranks that is compatible with the
> given
> box and a minimum cell size of 5.81734 nm
> Change the number of ranks or mdrun option -rdd or -dds
> Look in the log file for details on the domain decomposition
>
> On Mon, Mar 12, 2018 at 2:17 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 3/12/18 2:05 PM, Srinivasa Ramisetti wrote:
> >
> >> I think the minimum coordinates are (0,0,0)
> >>
> >>
> > Not really. GROMACS will accept negative coordinates and then re-wrap
> them
> > into the periodic box with its origin at (0,0,0).
> >
> > An actual error message and full command from the OP would be helpful
> here.
> >
> > -Justin
> >
> >
> > Srinivasa
> >> On 12/03/2018 18:01, Chhavi Yadav wrote:
> >>
> >>> Hi Justin,
> >>> Thanks for the reply.
> >>>
> >>> I meant this : In our application, we need to randomly sample
> coordinates
> >>> for atoms. When we were doing that, we got an error message for one of
> >>> the
> >>> random coordinate samples because the sample coordinate was smaller
> than
> >>> the minimum coordinates. What is this minimum coordinate and how can I
> >>> find
> >>> its value?
> >>>
> >>> I hope the question is clear now.
> >>>
> >>> Thanks,
> >>> Chhavi
> >>>
> >>> On Mon, Mar 12, 2018 at 1:43 PM, Justin Lemkul 
> wrote:
> >>>
> >>>
>  On 3/12/18 1:30 PM, Chhavi Yadav wrote:
> 
>  Hello,
> >
> > This is regarding the minimum size or resolution used in gromacs for
> > sampling coordinates of atoms. I know that the maximum size is the
> > matrix
> > box. Can someone please let me know what the minimum is?
> >
> > I'm not sure if this is the answer to your question, but GROMACS can
>  perform MD for any number of particles. The minimum box size depends
> on
>  the
>  cutoff values required for a given force field, as required by the
>  minimum
>  image convention, but one could simulate even a few atoms in the gas
>  phase
>  if desired.
> 
>  -Justin
> 
>  --
>  ==
> 
>  Justin A. Lemkul, Ph.D.
>  Assistant Professor
>  Virginia Tech Department of Biochemistry
> 
>  303 Engel Hall
>  340 West Campus Dr.
>  Blacksburg, VA 24061
> 
>  jalem...@vt.edu | (540) 231-3129
>  http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> 
>  ==
> 
>  --
>  Gromacs Users mailing list
> 
>  * Please search the archive at http://www.gromacs.org/Support
>  /Mailing_Lists/GMX-Users_List before posting!
> 
>  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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> 
> >>

Re: [gmx-users] nve simulation

Hi,

The list can't accept attachments.

There's a plot in the reference manual that shows some indicative minimal
drifts, which would be a good place to search. :-)

Mark

On Mon, Mar 12, 2018 at 9:31 PM Jo  wrote:

> Hello,
>
> I would like to run an NVE simulation but am having trouble conserving the
> energy.  From some past postings on the email list, I understand that some
> neighborlist buffer parameters need to be adjusted, however I still am not
> able to conserve energy.  I am simulating a box of 1000 SPCE water, and I
> also suspect 'settles' could be causing the lack of energy conservation.
> Can anyone provide any suggestions on what I can do to conserve energy?  I
> have attached the mdp file.
>
> Thank you,
>
> Jo
> --
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Re: [gmx-users] Regarding minimum size




On 3/12/18 4:52 PM, Chhavi Yadav wrote:

I wrote this code and was running the debugger:


int main(int argc, char *argv[]) {


 int rc;
 MD mdrunner;
 rc = mdrunner.mainFunction(argc, argv);
 printf("Potential Energy from integrator: %.6f\n", mdrunner.epot);

 mdrunner.epot = 0;

 t_state *t = mdrunner.globalState.get();
 t->x[0][0] = 10.0;
 t->x[0][1] = 10.0;
 t->x[0][2] = 10.0;


 rc = mdrunner.mainFunction(argc, argv);
 printf("Potential Energy from integrator: %.6f\n", mdrunner.epot);

 return rc;

}

OUTPUT:

Reading file 1aki/1AKI.tpr, VERSION
2018-dev-20180223-a989b355c-dirty-unknown (single precision)

NOTE: disabling dynamic load balancing as it is not supported in reruns.

No option -multi
No option -multi
No option -multi
No option -multi
No option -multi
No option -multi
No option -multi
No option -multi
Using 8 MPI threads
starting md rerun 'LYSOZYME', reading coordinates from input trajectory
'1aki/1AKI.gro'

Reading frames from gro file 'LYSOZYME;', 1960 atoms.

Reading frame   0 time0.000
WARNING: Some frames do not contain velocities.
  Ekin, temperature and pressure are incorrect,
  the virial will be incorrect when constraints are present.


Last frame  0 time0.000

Core t (s)   Wall t (s)(%)
Time:0.9610.120  800.0
  (ns/day)(hour/ns)
Performance:0.719   33.377
Potential Energy from integrator: -8519.961914

NOTE: disabling dynamic load balancing as it is not supported in reruns.


---
Program: GROMACS, version 2018-dev-20180308-65a7ab86c-dirty-unknown
Source file: src/gromacs/domdec/domdec.cpp (line 6571)
MPI rank:0 (out of 8)

Fatal error:
There is no domain decomposition for 8 ranks that is compatible with the
given
box and a minimum cell size of 5.81734 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition


The minimum cell size for domain decomposition is a function of the 
topology of the system. A system that requires a minimum cell size of 
5.8 nm is very unusual and suggests atypical topological elements. 
Please see the mailing list archive for possible solutions to this 
error; it comes up frequently and there are more details on 
http://www.gromacs.org/Documentation/Errors?highlight=errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] seeming paradox with gmx wham




On 3/12/18 3:42 PM, Alex wrote:
I actually understood your tutorial perfectly well. What I didn't 
expect is such a significant dependence on direction (assuming 
spherical symmetry clears the situation).


I also had to use direction-periodic instead of distance in your 
tutorial, because the box is 4 nm wide and grompp is screaming about 
distance exceeding half-box size. I used 5.0.3 before and it was fine 
with the 'distance' directive. I think 'direction-periodic' is also 
wrong for spherical symmetry. So, stick with distance and increase box 
size?


That's the easiest thing to do, yes, as long as the simulation is still 
reasonably efficient.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Regarding minimum size

2018-03-12 Thread Chhavi Yadav

I wrote this code and was running the debugger:


int main(int argc, char *argv[]) {


int rc;
MD mdrunner;
rc = mdrunner.mainFunction(argc, argv);
printf("Potential Energy from integrator: %.6f\n", mdrunner.epot);

mdrunner.epot = 0;

t_state *t = mdrunner.globalState.get();
t->x[0][0] = 10.0;
t->x[0][1] = 10.0;
t->x[0][2] = 10.0;


rc = mdrunner.mainFunction(argc, argv);
printf("Potential Energy from integrator: %.6f\n", mdrunner.epot);

return rc;

}

OUTPUT:

Reading file 1aki/1AKI.tpr, VERSION
2018-dev-20180223-a989b355c-dirty-unknown (single precision)

NOTE: disabling dynamic load balancing as it is not supported in reruns.

No option -multi
No option -multi
No option -multi
No option -multi
No option -multi
No option -multi
No option -multi
No option -multi
Using 8 MPI threads
starting md rerun 'LYSOZYME', reading coordinates from input trajectory
'1aki/1AKI.gro'

Reading frames from gro file 'LYSOZYME;', 1960 atoms.

Reading frame   0 time0.000
WARNING: Some frames do not contain velocities.
 Ekin, temperature and pressure are incorrect,
 the virial will be incorrect when constraints are present.


Last frame  0 time0.000

   Core t (s)   Wall t (s)(%)
   Time:0.9610.120  800.0
 (ns/day)(hour/ns)
Performance:0.719   33.377
Potential Energy from integrator: -8519.961914

NOTE: disabling dynamic load balancing as it is not supported in reruns.


---
Program: GROMACS, version 2018-dev-20180308-65a7ab86c-dirty-unknown
Source file: src/gromacs/domdec/domdec.cpp (line 6571)
MPI rank:0 (out of 8)

Fatal error:
There is no domain decomposition for 8 ranks that is compatible with the
given
box and a minimum cell size of 5.81734 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition

On Mon, Mar 12, 2018 at 2:17 PM, Justin Lemkul  wrote:

>
>
> On 3/12/18 2:05 PM, Srinivasa Ramisetti wrote:
>
>> I think the minimum coordinates are (0,0,0)
>>
>>
> Not really. GROMACS will accept negative coordinates and then re-wrap them
> into the periodic box with its origin at (0,0,0).
>
> An actual error message and full command from the OP would be helpful here.
>
> -Justin
>
>
> Srinivasa
>> On 12/03/2018 18:01, Chhavi Yadav wrote:
>>
>>> Hi Justin,
>>> Thanks for the reply.
>>>
>>> I meant this : In our application, we need to randomly sample coordinates
>>> for atoms. When we were doing that, we got an error message for one of
>>> the
>>> random coordinate samples because the sample coordinate was smaller than
>>> the minimum coordinates. What is this minimum coordinate and how can I
>>> find
>>> its value?
>>>
>>> I hope the question is clear now.
>>>
>>> Thanks,
>>> Chhavi
>>>
>>> On Mon, Mar 12, 2018 at 1:43 PM, Justin Lemkul  wrote:
>>>
>>>
 On 3/12/18 1:30 PM, Chhavi Yadav wrote:

 Hello,
>
> This is regarding the minimum size or resolution used in gromacs for
> sampling coordinates of atoms. I know that the maximum size is the
> matrix
> box. Can someone please let me know what the minimum is?
>
> I'm not sure if this is the answer to your question, but GROMACS can
 perform MD for any number of particles. The minimum box size depends on
 the
 cutoff values required for a given force field, as required by the
 minimum
 image convention, but one could simulate even a few atoms in the gas
 phase
 if desired.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Assistant Professor
 Virginia Tech Department of Biochemistry

 303 Engel Hall
 340 West Campus Dr.
 Blacksburg, VA 24061

 jalem...@vt.edu | (540) 231-3129
 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

 ==

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 Gromacs Users mailing list

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 /Mailing_Lists/GMX-Users_List before posting!

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 send a mail to gmx-users-requ...@gromacs.org.


>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> *

[gmx-users] nve simulation

2018-03-12 Thread Jo

Hello,

I would like to run an NVE simulation but am having trouble conserving the
energy.  From some past postings on the email list, I understand that some
neighborlist buffer parameters need to be adjusted, however I still am not
able to conserve energy.  I am simulating a box of 1000 SPCE water, and I
also suspect 'settles' could be causing the lack of energy conservation.
Can anyone provide any suggestions on what I can do to conserve energy?  I
have attached the mdp file.

Thank you,

Jo
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Re: [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?

2018-03-12 Thread Debdas Dhabal

Dear Mark,

Thanks for your response. Yes, I have gone through that document. (link:
http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf).

I have tried using energy-group pairs to take from table file and those are
not in the energygrps should take from Gromacs. But the document says that
the remaining interaction should be then calculated from default table file
named "table.xvg". Hence, in my case, if I only supply pair interaction
between *solute-solute* and* solute-solvent* (for which I need to customize
interaction) in *"table_solute_solute.xvg"* and default "*table.xvg"* file
respectively. Then Gromacs is taking *solvent-solvent* interaction (for
which I want to use the Gromacs normal thing and I haven't given a table
file) form that default *"table.xvg"* file. This means all the remaining
interaction (for which I haven't given the table file or didn't mention in
the energygrps)  is calculated using default "table.xvg" file. But this not
what I wanted. I want to take solvent-solvent interaction from Gromacs
defined LJ potential.

At the bottom of the page no 6 of that document also says that
"It is important to note however that when a combination of Lennard Jones
and Buckingham terms is required tabulated potentials must be used for all
the non-bonded interactions even for the Lennard Jones."

This means if I use *"vdwtype = User"* then I must have to supply all the
interaction using table file and cannot use both table and Gromacs defined
potential simultaneously ?. Kindly correct me if I got the meaning of that
line wrong.

I will be waiting for your valuable comments. Thanks so much

with regards
Debdas

On Mon, Mar 12, 2018 at 12:33 PM, Mark Abraham 
wrote:

> Hi,
>
> Yes, you can specify which energy-group pairs get which tables, and which
> do not get any (thus get the normal thing). Did you check out the
> documentation yet?
>
> Mark
>
> On Mon, Mar 12, 2018 at 5:30 PM Debdas Dhabal 
> wrote:
>
> > Hello everyone,
> >
> > Could anyone of you help me regarding the aforementioned problem. It
> would
> > be very nice of you.
> >
> > Thanks in advance.
> >
> > With regards
> > Debdas
> >
> > On Sat, Mar 10, 2018 at 1:30 PM, Debdas Dhabal 
> > wrote:
> >
> > > Dear Mark,
> > >
> > > Thanks  so much for your prompt reply. I had gone through that manual
> and
> > > I was able to use two different non-bonded potential for two different
> > > energy groups using table potential. But my question is a bit
> different.
> > > May be I was not able to make my question clear. I know the fact that
> by
> > > using table file I can use two different non bonded potential but what
> I
> > > wanted to ask whether it is possible to use table file only for user
> > > defined potential and not for which Gromacs already have predefined
> > > potential at the same time.
> > >
> > > Let me make it more clear. I have a system of solute in water. I want
> to
> > > use table file for only solute-water interaction and want to let the
> > > Gromacs take LJ potential for water-water interaction (ie. I don't want
> > to
> > > explicitly supply water-water interaction through Table file). In
> another
> > > way one can ask if I put *"vdwtype=User"* then is it *mandatory* to
> give
> > > non-bonded potential for both solute-water as well as water-water
> > > interaction through Table file only, or one can only use Table file for
> > > solute-water and Let the Gromacs take its predefined LJ potential form
> > for
> > > water-water interaction (as in case of vdwtype = Cut-Off case). So
> > > basically using Gromacs predefined potential and table potential at the
> > > same time.
> > >
> > > I hope I am able to make my question more clearer than before. Thanks
> > > again for your help.
> > >
> > > With regards
> > > Debdas
> > >
> > > On Sat, Mar 10, 2018 at 7:52 AM, Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > >
> > >> Hi,
> > >>
> > >> Yes, if you check out the documentation of tabulated non-bonded
> > >> interactions in the reference manual, you will see that you can apply
> > >> different tables for particles when drawn from different energy
> groups.
> > >>
> > >> Mark
> > >>
> > >> On Sat, Mar 10, 2018 at 1:06 AM Debdas Dhabal  >
> > >> wrote:
> > >>
> > >> > Hello everyone,
> > >> >
> > >> > This question may be very simple to most of the Gromacs user. I
> wonder
> > >> if
> > >> > Gromacs allow us to use both user-defined non-bonded potentials
> (Table
> > >> > potential) as well as Gromacs predefined potential at the same time.
> > For
> > >> > example, if I have a system with a solute in a solvent and for
> > >> > solvent-solvent nonbonded interaction, I want to use Gromacs defined
> > LJ
> > >> > potential but for solute-solvent nonbonded interaction, I want to
> use
> > a
> > >> > custom potential using a Table format. I know that solvent-solvent
> > >> > interaction can also be incorporated in the Table file and we can
> run
> > >> > Gromacs successfully, but I want to use Table potential only

Re: [gmx-users] seeming paradox with gmx wham


Sorry, i meant 4 nm tall, not wide.


On 3/12/2018 1:42 PM, Alex wrote:
I actually understood your tutorial perfectly well. What I didn't 
expect is such a significant dependence on direction (assuming 
spherical symmetry clears the situation).


I also had to use direction-periodic instead of distance in your 
tutorial, because the box is 4 nm wide and grompp is screaming about 
distance exceeding half-box size. I used 5.0.3 before and it was fine 
with the 'distance' directive. I think 'direction-periodic' is also 
wrong for spherical symmetry. So, stick with distance and increase box 
size?


Thanks,

Alex


On 3/12/2018 1:35 PM, Justin Lemkul wrote:



On 3/12/18 3:28 PM, Alex wrote:

Thanks!

Just to make sure I'm doing this right this time. By merely changing 
the dim directive with everything else following your tutorial, I 
would be probing the spherical domain around the pore with a bunch 
of different radius values? Because this is exactly what I want.




Yes, you're applying a 1-D bias when you actually want a 3-D bias. 
People often misuse the tutorial .mdp files, though I will have a new 
version of the tutorial out this summer (along with a paper) that 
should clear all this up.


-Justin


Thanks,

Alex


On 3/12/2018 8:43 AM, Justin Lemkul wrote:



On 3/11/18 8:05 PM, Alex wrote:
Just to add to my question... The pull code for the umbrella 
sampling from each of the N configs, as used in Justin's tutorial, is


pull_coord1_type    = umbrella
pull_coord1_geometry    = distance
...
pull_coord1_dim = N N Y

So, in each of the generated pullf and pullx files we sample a 
flat slice at a given Z, and the reported forces and displacements 
are along Z. What appears to be the reaction coordinate in our 
case is the radius from the pore mouth, and one has to sample a 
set of hemispheres from a series of radius values. Is this at all 
a possibility?




Yes, but not by following the tutorial. You'd need to use 
pull_coord1_dim = Y Y Y to restrict the ions to a given radius 
around the pore itself. As it is, you're probably underestimating 
entropic contributions to the free energy.


-Justin









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Re: [gmx-users] seeming paradox with gmx wham

I actually understood your tutorial perfectly well. What I didn't expect 
is such a significant dependence on direction (assuming spherical 
symmetry clears the situation).


I also had to use direction-periodic instead of distance in your 
tutorial, because the box is 4 nm wide and grompp is screaming about 
distance exceeding half-box size. I used 5.0.3 before and it was fine 
with the 'distance' directive. I think 'direction-periodic' is also 
wrong for spherical symmetry. So, stick with distance and increase box size?


Thanks,

Alex


On 3/12/2018 1:35 PM, Justin Lemkul wrote:



On 3/12/18 3:28 PM, Alex wrote:

Thanks!

Just to make sure I'm doing this right this time. By merely changing 
the dim directive with everything else following your tutorial, I 
would be probing the spherical domain around the pore with a bunch of 
different radius values? Because this is exactly what I want.




Yes, you're applying a 1-D bias when you actually want a 3-D bias. 
People often misuse the tutorial .mdp files, though I will have a new 
version of the tutorial out this summer (along with a paper) that 
should clear all this up.


-Justin


Thanks,

Alex


On 3/12/2018 8:43 AM, Justin Lemkul wrote:



On 3/11/18 8:05 PM, Alex wrote:
Just to add to my question... The pull code for the umbrella 
sampling from each of the N configs, as used in Justin's tutorial, is


pull_coord1_type    = umbrella
pull_coord1_geometry    = distance
...
pull_coord1_dim = N N Y

So, in each of the generated pullf and pullx files we sample a flat 
slice at a given Z, and the reported forces and displacements are 
along Z. What appears to be the reaction coordinate in our case is 
the radius from the pore mouth, and one has to sample a set of 
hemispheres from a series of radius values. Is this at all a 
possibility?




Yes, but not by following the tutorial. You'd need to use 
pull_coord1_dim = Y Y Y to restrict the ions to a given radius 
around the pore itself. As it is, you're probably underestimating 
entropic contributions to the free energy.


-Justin







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Re: [gmx-users] seeming paradox with gmx wham




On 3/12/18 3:28 PM, Alex wrote:

Thanks!

Just to make sure I'm doing this right this time. By merely changing 
the dim directive with everything else following your tutorial, I 
would be probing the spherical domain around the pore with a bunch of 
different radius values? Because this is exactly what I want.




Yes, you're applying a 1-D bias when you actually want a 3-D bias. 
People often misuse the tutorial .mdp files, though I will have a new 
version of the tutorial out this summer (along with a paper) that should 
clear all this up.


-Justin


Thanks,

Alex


On 3/12/2018 8:43 AM, Justin Lemkul wrote:



On 3/11/18 8:05 PM, Alex wrote:
Just to add to my question... The pull code for the umbrella 
sampling from each of the N configs, as used in Justin's tutorial, is


pull_coord1_type    = umbrella
pull_coord1_geometry    = distance
...
pull_coord1_dim = N N Y

So, in each of the generated pullf and pullx files we sample a flat 
slice at a given Z, and the reported forces and displacements are 
along Z. What appears to be the reaction coordinate in our case is 
the radius from the pore mouth, and one has to sample a set of 
hemispheres from a series of radius values. Is this at all a 
possibility?




Yes, but not by following the tutorial. You'd need to use 
pull_coord1_dim = Y Y Y to restrict the ions to a given radius around 
the pore itself. As it is, you're probably underestimating entropic 
contributions to the free energy.


-Justin





--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Sudden increase in RMSD values for 100ns simulation of protein-protein complex




On 3/12/18 3:26 PM, SHYANTANI MAITI wrote:

Dear all,
I have been simulating a protein-protein complex using gromacs for 100ns.
after the completion of job, I find that the rmsd values have undergone a
sudden increase after 20ns of the simulation. Is my simulation going wrong
somewhere? Can protein-protein complexes be simulated in gromacs?
Following is the final mdp file for simulating my protein-protein complex.



Probably a PBC issue. Use trjconv to re-center everything before 
computing RMSD.


-Justin


title= MD simulation
; Run parameters
integrator= md; leap-frog integrator
nsteps= 5000; 2 * 5000 = 10 ps (100 ns)
dt= 0.002; 2 fs
; Output control
nstxout= 5000; save coordinates every 10.0 ps
nstvout= 5000; save velocities every 10.0 ps
nstenergy= 5000; save energies every 10.0 ps
nstlog= 5000; update log file every 10.0 ps
nstxout-compressed  = 5000  ; save compressed coordinates every 10.0 ps
 ; nstxout-compressed replaces nstxtcout
compressed-x-grps   = System; replaces xtc-grps
; Bond parameters
continuation= yes; Restarting after NPT
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
cutoff-scheme   = Verlet
ns_type= grid; search neighboring grid cells
nstlist= 10; 20 fs, largely irrelevant with Verlet
scheme
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; 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= V-rescale; modified Berendsen thermostat
tc-grps= Protein Non-Protein; two coupling groups - more
accurate
tau_t= 0.1  0.1; time constant, in ps
ref_t= 300   300; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl= Berendsen; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box
vectors
tau_p= 2.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of
water, 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





--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] seeming paradox with gmx wham


Thanks!

Just to make sure I'm doing this right this time. By merely changing the 
dim directive with everything else following your tutorial, I would be 
probing the spherical domain around the pore with a bunch of different 
radius values? Because this is exactly what I want.


Thanks,

Alex


On 3/12/2018 8:43 AM, Justin Lemkul wrote:



On 3/11/18 8:05 PM, Alex wrote:
Just to add to my question... The pull code for the umbrella sampling 
from each of the N configs, as used in Justin's tutorial, is


pull_coord1_type    = umbrella
pull_coord1_geometry    = distance
...
pull_coord1_dim = N N Y

So, in each of the generated pullf and pullx files we sample a flat 
slice at a given Z, and the reported forces and displacements are 
along Z. What appears to be the reaction coordinate in our case is 
the radius from the pore mouth, and one has to sample a set of 
hemispheres from a series of radius values. Is this at all a 
possibility?




Yes, but not by following the tutorial. You'd need to use 
pull_coord1_dim = Y Y Y to restrict the ions to a given radius around 
the pore itself. As it is, you're probably underestimating entropic 
contributions to the free energy.


-Justin



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[gmx-users] Sudden increase in RMSD values for 100ns simulation of protein-protein complex

2018-03-12 Thread SHYANTANI MAITI

Dear all,
I have been simulating a protein-protein complex using gromacs for 100ns.
after the completion of job, I find that the rmsd values have undergone a
sudden increase after 20ns of the simulation. Is my simulation going wrong
somewhere? Can protein-protein complexes be simulated in gromacs?
Following is the final mdp file for simulating my protein-protein complex.


title= MD simulation
; Run parameters
integrator= md; leap-frog integrator
nsteps= 5000; 2 * 5000 = 10 ps (100 ns)
dt= 0.002; 2 fs
; Output control
nstxout= 5000; save coordinates every 10.0 ps
nstvout= 5000; save velocities every 10.0 ps
nstenergy= 5000; save energies every 10.0 ps
nstlog= 5000; update log file every 10.0 ps
nstxout-compressed  = 5000  ; save compressed coordinates every 10.0 ps
; nstxout-compressed replaces nstxtcout
compressed-x-grps   = System; replaces xtc-grps
; Bond parameters
continuation= yes; Restarting after NPT
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
cutoff-scheme   = Verlet
ns_type= grid; search neighboring grid cells
nstlist= 10; 20 fs, largely irrelevant with Verlet
scheme
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; 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= V-rescale; modified Berendsen thermostat
tc-grps= Protein Non-Protein; two coupling groups - more
accurate
tau_t= 0.1  0.1; time constant, in ps
ref_t= 300   300; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl= Berendsen; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box
vectors
tau_p= 2.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of
water, 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



-- 
Best regards,
*Shyantani Maiti*
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Re: [gmx-users] Regarding minimum size




On 3/12/18 2:05 PM, Srinivasa Ramisetti wrote:

I think the minimum coordinates are (0,0,0)



Not really. GROMACS will accept negative coordinates and then re-wrap 
them into the periodic box with its origin at (0,0,0).


An actual error message and full command from the OP would be helpful here.

-Justin


Srinivasa
On 12/03/2018 18:01, Chhavi Yadav wrote:

Hi Justin,
Thanks for the reply.

I meant this : In our application, we need to randomly sample 
coordinates
for atoms. When we were doing that, we got an error message for one 
of the

random coordinate samples because the sample coordinate was smaller than
the minimum coordinates. What is this minimum coordinate and how can 
I find

its value?

I hope the question is clear now.

Thanks,
Chhavi

On Mon, Mar 12, 2018 at 1:43 PM, Justin Lemkul  wrote:



On 3/12/18 1:30 PM, Chhavi Yadav wrote:


Hello,

This is regarding the minimum size or resolution used in gromacs for
sampling coordinates of atoms. I know that the maximum size is the 
matrix

box. Can someone please let me know what the minimum is?


I'm not sure if this is the answer to your question, but GROMACS can
perform MD for any number of particles. The minimum box size depends 
on the
cutoff values required for a given force field, as required by the 
minimum
image convention, but one could simulate even a few atoms in the gas 
phase

if desired.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Regarding minimum size

2018-03-12 Thread Srinivasa Ramisetti


I think the minimum coordinates are (0,0,0)

Srinivasa
On 12/03/2018 18:01, Chhavi Yadav wrote:

Hi Justin,
Thanks for the reply.

I meant this : In our application, we need to randomly sample coordinates
for atoms. When we were doing that, we got an error message for one of the
random coordinate samples because the sample coordinate was smaller than
the minimum coordinates. What is this minimum coordinate and how can I find
its value?

I hope the question is clear now.

Thanks,
Chhavi

On Mon, Mar 12, 2018 at 1:43 PM, Justin Lemkul  wrote:



On 3/12/18 1:30 PM, Chhavi Yadav wrote:


Hello,

This is regarding the minimum size or resolution used in gromacs for
sampling coordinates of atoms. I know that the maximum size is the matrix
box. Can someone please let me know what the minimum is?


I'm not sure if this is the answer to your question, but GROMACS can
perform MD for any number of particles. The minimum box size depends on the
cutoff values required for a given force field, as required by the minimum
image convention, but one could simulate even a few atoms in the gas phase
if desired.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Regarding minimum size

2018-03-12 Thread Chhavi Yadav

Hi Justin,
Thanks for the reply.

I meant this : In our application, we need to randomly sample coordinates
for atoms. When we were doing that, we got an error message for one of the
random coordinate samples because the sample coordinate was smaller than
the minimum coordinates. What is this minimum coordinate and how can I find
its value?

I hope the question is clear now.

Thanks,
Chhavi

On Mon, Mar 12, 2018 at 1:43 PM, Justin Lemkul  wrote:

>
>
> On 3/12/18 1:30 PM, Chhavi Yadav wrote:
>
>> Hello,
>>
>> This is regarding the minimum size or resolution used in gromacs for
>> sampling coordinates of atoms. I know that the maximum size is the matrix
>> box. Can someone please let me know what the minimum is?
>>
>
> I'm not sure if this is the answer to your question, but GROMACS can
> perform MD for any number of particles. The minimum box size depends on the
> cutoff values required for a given force field, as required by the minimum
> image convention, but one could simulate even a few atoms in the gas phase
> if desired.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
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>
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Re: [gmx-users] Regarding minimum size




On 3/12/18 1:30 PM, Chhavi Yadav wrote:

Hello,

This is regarding the minimum size or resolution used in gromacs for
sampling coordinates of atoms. I know that the maximum size is the matrix
box. Can someone please let me know what the minimum is?


I'm not sure if this is the answer to your question, but GROMACS can 
perform MD for any number of particles. The minimum box size depends on 
the cutoff values required for a given force field, as required by the 
minimum image convention, but one could simulate even a few atoms in the 
gas phase if desired.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Help with interpreting message for fatal error

2018-03-12 Thread Viveca Lindahl

Hi Gregory,

It's periodically connected and I am applying adaptive biasing/pulling
(forgot to say). If you have special experience with that kind of setup,
I'd be interested in hearing it. Otherwise, it's quite standard, and yes,
parmbsc1.

--
Viveca


On Mon, Mar 12, 2018 at 6:53 PM, Gregory Poon  wrote:

> Hi Viveca,
>
> Could you share more details of your simulations that may shed any light?
> I assume that you are using parmbsc1 as the DNA forcefield.  Is it an
> "unusual" system?  We (and I am sure others) simulate DNA (± ligand) quite
> a bit and would be as interested in understanding what is going wrong here,
> although I have never encountered what you are observing.
>
> Best wishes,
>
> Gregory
>
>
>
> On 3/12/2018 7:42 AM, Viveca Lindahl wrote:
>
>> Hi Gregory,
>>
>> In the sense that I see it happening repeatedly yes :) But I can't
>> reproduce it very predictably.
>>
>> After seeing that (for my small system) I get very large box vector
>> fluctuations using Parrinello-Rahman, my current assumption is that there
>> are some stability assumptions made by mdrun internally that are being
>> violated.
>> I would still be interested in understanding what actually goes wrong
>> though.
>>
>> --
>> Viveca
>>
>>
>> On Mon, Mar 12, 2018 at 4:49 PM, Gregory Poon  wrote:
>>
>> Since there hasn't been any response to your question yet, may I ask: is
>>> it reproducible?
>>>
>>> Gregory
>>>
>>>
>>> On 3/11/2018 7:30 AM, Viveca Lindahl wrote:
>>>
>>> Hi,

 I'm running a simulation of a periodic DNA molecule. After some time I
 get,
 sometimes the following error message:

 ---

 A list of missing interactions:
Proper Dih. of   3917 missing  1

 Molecule type 'DNA_chain_A'
 the first 10 missing interactions, except for exclusions:
Proper Dih. atoms  414  417  418  421 global   414   417
  418
 421

 ---
 Program: gmx mdrun, version 2018.1-dev-20180306-33093601f
 Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
 MPI rank:0 (out of 32)

 Fatal error:
 1 of the 10381 bonded interactions could not be calculated because some
 atoms
 involved moved further apart than the multi-body cut-off distance
 (0.5465
 nm)
 or the two-body cut-off distance (1.093 nm), see option -rdd, for pairs
 and
 tabulated bonds also see option -ddcheck

 For more information and tips for troubleshooting, please check the
 GROMACS
 website at https://na01.safelinks.protection.outlook.com/?url=http%3A%
 2F%2Fwww.gromacs.org%2FDocumentation%2FErrors&data=02%7C01%
 7Cgpoon%40gsu.edu%7C18eac9ccdd4b479d86c708d5875cbb61%7C515ad
 73d8d5e4169895c9789dc742a70%7C0%7C0%7C636563754716997653&
 sdata=wUdEASAxNIPHNAmQwBO8EO0Ec8EI%2FVdjY7f7i9R0IYc%3D&reserved=0
 ---
 Rank 0 [Sun Mar 11 13:37:32 2018] [c0-0c1s3n0] application called
 MPI_Abort(MPI_COMM_WORLD, 1) - process 0
 _pmiu_daemon(SIGCHLD): [NID 00076] [c0-0c1s3n0] [Sun Mar 11 13:37:32
 2018]
 PE RANK 0 exit signal Aborted
 [NID 00076] 2018-03-11 13:37:32 Apid 12709959: initiated application
 termination
 Application 12709959 exit codes: 134
 Application 12709959 resources: utime ~1083s, stime ~16s, Rss ~21376,
 inblocks ~34261, outblocks ~55016
 ---> Reached end of run script.


 How should I... proceed here? Is my system set up poorly, is it a bug in
 mdrun? Suggestions appreciated.

 --
 Viveca

 --
>>>
>>> *Gregory M. K. Poon, PhD, RPh*
>>> Associate Professor
>>> Departments of Chemistry and Nutrition | Georgia State University
>>> NSC 414/415/416 | 50 Decatur St. SE, Atlanta, GA 30302
>>> P.O. Box 3965 | Atlanta, GA 30303
>>> Ph (404) 413-5491 | gp...@gsu.edu 
>>>
>>> --
>>> Gromacs Users mailing list
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>>> * Please search the archive at https://na01.safelinks.protect
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>>> 8827d1c4%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C636564
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Re: [gmx-users] Help with interpreting message for fatal error




On 3/12/18 1:40 PM, Viveca Lindahl wrote:

Hi Justin,

I'm using semi-isotropic pressure coupling and the periodicity is along z. I
should say that I'm also adaptively biasing a base pair to open, which is
triggering the fluctuations.

I guess you mean using only OpenMP? I have not tried that no, thanks for
the suggestion. Now I changed to Berendsen coupling which avoids the
problem (at least the fatal errors).


Yes, the problem is coming from either DD bookkeeping or actual 
instability. Trying with only OpenMP parallelization and therefore no 
domains will sort out whether it's physical or just a software problem. 
There's a lot going on if you've got periodic molecules, NPT, and a 
biasing potential, all with DD. Probably something no one has ever 
tested in GROMACS.


-Justin


--
Viveca


On Mon, Mar 12, 2018 at 3:46 PM, Justin Lemkul  wrote:



On 3/12/18 10:42 AM, Viveca Lindahl wrote:


Hi Gregory,

In the sense that I see it happening repeatedly yes :) But I can't
reproduce it very predictably.

After seeing that (for my small system) I get very large box vector
fluctuations using Parrinello-Rahman, my current assumption is that there
are some stability assumptions made by mdrun internally that are being
violated.
I would still be interested in understanding what actually goes wrong
though.


Periodic molecules are usually used in CNT systems or similar, and the
typical advice is to not apply pressure coupling along the long axis. I
suspect interactions get lost when the box fluctuates and the domain
topology does not get updated correctly. Does it work correctly with OpenMP?

-Justin


--

Viveca


On Mon, Mar 12, 2018 at 4:49 PM, Gregory Poon  wrote:

Since there hasn't been any response to your question yet, may I ask: is

it reproducible?

Gregory


On 3/11/2018 7:30 AM, Viveca Lindahl wrote:

Hi,

I'm running a simulation of a periodic DNA molecule. After some time I
get,
sometimes the following error message:

---

A list of missing interactions:
Proper Dih. of   3917 missing  1

Molecule type 'DNA_chain_A'
the first 10 missing interactions, except for exclusions:
Proper Dih. atoms  414  417  418  421 global   414   417
  418
421

---
Program: gmx mdrun, version 2018.1-dev-20180306-33093601f
Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
MPI rank:0 (out of 32)

Fatal error:
1 of the 10381 bonded interactions could not be calculated because some
atoms
involved moved further apart than the multi-body cut-off distance
(0.5465
nm)
or the two-body cut-off distance (1.093 nm), see option -rdd, for pairs
and
tabulated bonds also see option -ddcheck

For more information and tips for troubleshooting, please check the
GROMACS
website at https://na01.safelinks.protection.outlook.com/?url=http%3A%
2F%2Fwww.gromacs.org%2FDocumentation%2FErrors&data=02%7C01%
7Cgpoon%40gsu.edu%7C18eac9ccdd4b479d86c708d5875cbb61%7C515ad
73d8d5e4169895c9789dc742a70%7C0%7C0%7C636563754716997653&
sdata=wUdEASAxNIPHNAmQwBO8EO0Ec8EI%2FVdjY7f7i9R0IYc%3D&reserved=0
---
Rank 0 [Sun Mar 11 13:37:32 2018] [c0-0c1s3n0] application called
MPI_Abort(MPI_COMM_WORLD, 1) - process 0
_pmiu_daemon(SIGCHLD): [NID 00076] [c0-0c1s3n0] [Sun Mar 11 13:37:32
2018]
PE RANK 0 exit signal Aborted
[NID 00076] 2018-03-11 13:37:32 Apid 12709959: initiated application
termination
Application 12709959 exit codes: 134
Application 12709959 resources: utime ~1083s, stime ~16s, Rss ~21376,
inblocks ~34261, outblocks ~55016
---> Reached end of run script.


How should I... proceed here? Is my system set up poorly, is it a bug in
mdrun? Suggestions appreciated.

--
Viveca

--

*Gregory M. K. Poon, PhD, RPh*
Associate Professor
Departments of Chemistry and Nutrition | Georgia State University
NSC 414/415/416 | 50 Decatur St. SE, Atlanta, GA 30302
P.O. Box 3965 | Atlanta, GA 30303
Ph (404) 413-5491 | gp...@gsu.edu 

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Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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Re: [gmx-users] Help with interpreting message for fatal error

2018-03-12 Thread Viveca Lindahl

Hi Justin,

I'm using semi-isotropic pressure coupling and the periodicity is along z. I
should say that I'm also adaptively biasing a base pair to open, which is
triggering the fluctuations.

I guess you mean using only OpenMP? I have not tried that no, thanks for
the suggestion. Now I changed to Berendsen coupling which avoids the
problem (at least the fatal errors).

--
Viveca


On Mon, Mar 12, 2018 at 3:46 PM, Justin Lemkul  wrote:

>
>
> On 3/12/18 10:42 AM, Viveca Lindahl wrote:
>
>> Hi Gregory,
>>
>> In the sense that I see it happening repeatedly yes :) But I can't
>> reproduce it very predictably.
>>
>> After seeing that (for my small system) I get very large box vector
>> fluctuations using Parrinello-Rahman, my current assumption is that there
>> are some stability assumptions made by mdrun internally that are being
>> violated.
>> I would still be interested in understanding what actually goes wrong
>> though.
>>
>
> Periodic molecules are usually used in CNT systems or similar, and the
> typical advice is to not apply pressure coupling along the long axis. I
> suspect interactions get lost when the box fluctuates and the domain
> topology does not get updated correctly. Does it work correctly with OpenMP?
>
> -Justin
>
>
> --
>> Viveca
>>
>>
>> On Mon, Mar 12, 2018 at 4:49 PM, Gregory Poon  wrote:
>>
>> Since there hasn't been any response to your question yet, may I ask: is
>>> it reproducible?
>>>
>>> Gregory
>>>
>>>
>>> On 3/11/2018 7:30 AM, Viveca Lindahl wrote:
>>>
>>> Hi,

 I'm running a simulation of a periodic DNA molecule. After some time I
 get,
 sometimes the following error message:

 ---

 A list of missing interactions:
Proper Dih. of   3917 missing  1

 Molecule type 'DNA_chain_A'
 the first 10 missing interactions, except for exclusions:
Proper Dih. atoms  414  417  418  421 global   414   417
  418
 421

 ---
 Program: gmx mdrun, version 2018.1-dev-20180306-33093601f
 Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
 MPI rank:0 (out of 32)

 Fatal error:
 1 of the 10381 bonded interactions could not be calculated because some
 atoms
 involved moved further apart than the multi-body cut-off distance
 (0.5465
 nm)
 or the two-body cut-off distance (1.093 nm), see option -rdd, for pairs
 and
 tabulated bonds also see option -ddcheck

 For more information and tips for troubleshooting, please check the
 GROMACS
 website at https://na01.safelinks.protection.outlook.com/?url=http%3A%
 2F%2Fwww.gromacs.org%2FDocumentation%2FErrors&data=02%7C01%
 7Cgpoon%40gsu.edu%7C18eac9ccdd4b479d86c708d5875cbb61%7C515ad
 73d8d5e4169895c9789dc742a70%7C0%7C0%7C636563754716997653&
 sdata=wUdEASAxNIPHNAmQwBO8EO0Ec8EI%2FVdjY7f7i9R0IYc%3D&reserved=0
 ---
 Rank 0 [Sun Mar 11 13:37:32 2018] [c0-0c1s3n0] application called
 MPI_Abort(MPI_COMM_WORLD, 1) - process 0
 _pmiu_daemon(SIGCHLD): [NID 00076] [c0-0c1s3n0] [Sun Mar 11 13:37:32
 2018]
 PE RANK 0 exit signal Aborted
 [NID 00076] 2018-03-11 13:37:32 Apid 12709959: initiated application
 termination
 Application 12709959 exit codes: 134
 Application 12709959 resources: utime ~1083s, stime ~16s, Rss ~21376,
 inblocks ~34261, outblocks ~55016
 ---> Reached end of run script.


 How should I... proceed here? Is my system set up poorly, is it a bug in
 mdrun? Suggestions appreciated.

 --
 Viveca

 --
>>>
>>> *Gregory M. K. Poon, PhD, RPh*
>>> Associate Professor
>>> Departments of Chemistry and Nutrition | Georgia State University
>>> NSC 414/415/416 | 50 Decatur St. SE, Atlanta, GA 30302
>>> P.O. Box 3965 | Atlanta, GA 30303
>>> Ph (404) 413-5491 | gp...@gsu.edu 
>>>
>>> --
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>>>
>>> * Please search the archive at http://www.gromacs.org/Support
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
>
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[gmx-users] Regarding minimum size

2018-03-12 Thread Chhavi Yadav

Hello,

This is regarding the minimum size or resolution used in gromacs for
sampling coordinates of atoms. I know that the maximum size is the matrix
box. Can someone please let me know what the minimum is?

Thanks,
Chhavi
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Re: [gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?

Hi,

On Mon, Mar 12, 2018 at 4:19 PM Douwe Pollmann 
wrote:

> Dear Gromacs users,
>
> I am currently working on a coarse-grained model where I want to fix atoms
> (Cb's) on a certain distance from Ca-Ca bonds, so that they can rotate
> freely. This freedom will be restricted by a dihedral that determines the
> relative orientation between the Cb's.
> I am using distance constraints or (non-chemical) bonds between a Cb and
> the adjacent Ca's, so that a fixed triangle is formed. I assumed that with
> this method the distance from Cb to the Ca-Ca bond should be correct and
> that my problem was solved. However, sometimes my simulations crash, and it
> appears that both constraint algorithms (LINCS and SHAKE) are not able to
> deal with angle constraints / 3 atoms bonded in a triangle.
>

You should double check the documentation of the mdp options relevant to
these algorithms so that you know you are using them correctly - triangles
of constraints are more demanding than uncoupled ones.

You should also make sure that your exclusions are appropriate. If the Cb
atom is having a non-bonded interaction with the Ca atoms (or their
neighbours) then you make life hard on the constraint implementation.

> I came up with two (maybe very strange) idea to solve this problem:
> 1: There is a third algorithm to solve constraints, called SETTLE, but it
> is stated almost everywhere that it is useful for water molecules. Do you
> know if it is possible to use SETTLE in other molecules than water, for
> example in my system? The Cb would be the "O", and the Ca's the "H's".
>

No, SETTLE is specific to water, ie. molecules with three heavy atoms.

> 2: Is it possible to disable the constraint solver, so that neither Lincs
> and Shake are used? I am asking this because someone mentioned that the
> solvers are meant to reduce the very fast vibrations of light atoms, so
> that a larger mass on my Cb's will also solve the problem.
>

If you don't want constraints, don't ask for any :-) You also won't get
your fixed triangle. You can of course do that, with due regard to your
timestep and validation of your module.

For the method I want to use I really need the Cb's at fixed distances from
> the Ca's and the Ca-Ca bond, but I cannot think of any way without
> triangular constraints that fulfils these requirements.
>
> Does any of you know the answers to the two possible solutions, or a way to
> fix the distance between Cb and the Ca-Ca bond, while maintaining the free
> rotation?
>

The ideal answer would be to use a virtual site in GROMACS, but there's no
way of constructing the Cb atom off the line of the two Ca atoms. There are
ways to construct the Cb atom on the line, or various ways from the
positions of three or more other atoms, but nothing is clearly suitable for
your case, unfortunately.

Mark

Thank you in advance for any help!
>
> Kind regards,
> Douwe Pollmann
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[gmx-users] Free energy perturbation for larger molecule - big Coulomb solvation energies

2018-03-12 Thread Krzysztof Makuch

Hello!

I am trying to calculate solvation energy, using Free Energy Perturbation
for lutein in water and bilayer. Simulation runs smoothly, but Coulomb part
of calculated energy is extremly high for hydrophobic molecule
(C40H54(OH)2): above 40kcal/mol // 180 kJ/mol both in water and bilayer. I
am working with topology, with OPLS-AA charges.

To check possibility if the charges are somehow wrong I've parametrized
molecule with automatic server for charmm - cgenff. Parametrization of the
molecule in charmm clearly isn't perfect, but since what I want is only
rough estimation of possibility of wrong OPLS-AA charges it should be
sufficient. However, I am still getting even higher value of 300kJ/mol.
I've also checked methanol under same conditions in mdp file and obtained
results were reasonable.

Now, I suspect I've messed something in mdp FEP settings,could you please
look at it and give me a hint, what may be wrong with these?

Best,
Krzysiek

; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.002
nsteps   = 175   ; 3.5 ns
nstcomm  = 100
; Output control
nstxout  = 500
nstvout  = 500
nstfout  = 0
nstlog   = 500
nstenergy= 500
nstxout-compressed   = 0
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme= verlet
nstlist  = 20
ns_type  = grid
pbc  = xyz
rlist= 1.2
; Electrostatics
coulombtype  = PME
rcoulomb = 1.2
; van der Waals
vdwtype  = cutoff
vdw-modifier = potential-switch
rvdw-switch  = 1.0
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.1
; EWALD/PME/PPPM parameters
pme_order= 5
ewald_rtol   = 1e-06
epsilon_surface  = 0
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = System
tau_t= 0.6
ref_t= 310
; Pressure coupling is on for NPT
Pcoupl   = Parrinello-Rahman
pcoupltype = isotropic
tau_p= 1.0
compressibility  = 4.5e-05
ref_p= 1.0
; Free energy control stuff
free_energy  = yes
init_lambda_state= 0
delta_lambda = 0
calc_lambda_neighbors= 1; only immediate neighboring windows
; Vectors of lambda specified here
; Each combination is an index that is retrieved from init_lambda_state for
each simulation
; init_lambda_state012345
678910   11   12   13
14   15   16   17   18   19   20
vdw_lambdas  = 000000000
000000000000
coul_lambdas = 00.050.10.150.20.25
0.30.350.40.450.50.550.60.650.70.75
0.80.850.90.951
; We are not transforming any bonded or restrained interactions
bonded_lambdas   = 000000000
000000000000
restraint_lambdas= 000000000
000000000000
; Masses are not changing (particle identities are the same at lambda = 0
and lambda = 1)
mass_lambdas = 000000000
000000000000
; Not doing simulated temperting here
temperature_lambdas  = 000000000
000000000000
; Options for the decoupling
sc-alpha = 0.5
sc-coul  = no   ; linear interpolation of Coulomb (none
in this case)
sc-power = 1
sc-sigma = 0.3
couple-moltype   = lutein  ; name of moleculetype to decouple
couple-lambda0   = vdw-q  ; all
couple-lambda1   = vdw ; vdw
couple-intramol  = yes
nstdhdl  = 100
; No velocities during EM
gen_vel  = no
; options for bonds
constraints  = h-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Do not constrain the starting configuration
continuation = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 4

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Re: [gmx-users] RESTARTING THE CALCULATION

Hi,

Then maybe the file is corrupted. What does gmx check say about it?

Mark

On Mon, Mar 12, 2018, 17:45 Neha Gupta  wrote:

> Hi,
>
> I gave
>
> gmx mdrun -s md.tpr -cpi md_step17960400.cpt
>
> It says, Checkpoint file corrupted or truncated or you are out of disk
> space?
>
> I have deleted files of higher MB. Why the problem persists?
>
> Thanks,
> Neha
>
> On Sun, Mar 11, 2018 at 10:55 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Exactly as you ran the original simulation, plus pass the name of the
> > latest checkpoint file to -cpi. Back up your files first.
> >
> > Mark
> >
> > On Sun, Mar 11, 2018 at 6:18 PM Neha Gupta 
> > wrote:
> >
> > > Hi gromacs users,
> > >
> > > I wanted to do simulations fro 50 ns.
> > >
> > > But, due to lack of disk space, it abruptly stopped.
> > >
> > >
> > > I have md.xtc, md.cpt, md.log, md_step17960400.cpt, md_prev.cpt.
> > >
> > > How to restart the calculation and complete it successfully?
> > >
> > > Thanks,
> > > Neha
> > > --
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Re: [gmx-users] RESTARTING THE CALCULATION

2018-03-12 Thread Neha Gupta

Hi,

I gave

gmx mdrun -s md.tpr -cpi md_step17960400.cpt

It says, Checkpoint file corrupted or truncated or you are out of disk
space?

I have deleted files of higher MB. Why the problem persists?

Thanks,
Neha

On Sun, Mar 11, 2018 at 10:55 PM, Mark Abraham 
wrote:

> Hi,
>
> Exactly as you ran the original simulation, plus pass the name of the
> latest checkpoint file to -cpi. Back up your files first.
>
> Mark
>
> On Sun, Mar 11, 2018 at 6:18 PM Neha Gupta 
> wrote:
>
> > Hi gromacs users,
> >
> > I wanted to do simulations fro 50 ns.
> >
> > But, due to lack of disk space, it abruptly stopped.
> >
> >
> > I have md.xtc, md.cpt, md.log, md_step17960400.cpt, md_prev.cpt.
> >
> > How to restart the calculation and complete it successfully?
> >
> > Thanks,
> > Neha
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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Re: [gmx-users] Problems in putting restraints during free energy perturbation calculations

2018-03-12 Thread Searle Duay

Hi Mark,

Thanks for reminding me about this. Yes, I've read up on this on a tutorial
and I probably interchanged which interactions should be turned on first.

Thank you again. Have a wonderful day!

Searle

On Mon, Mar 12, 2018 at 12:32 PM, Mark Abraham 
wrote:

> Hi,
>
> Don't do that. You have charges on atoms that have no VDW, so there is
> nothing to stop them flying all over the place and imparting crazy forces
> on other atoms that have VDW, etc. Turn the VDW fully on before adding any
> charge. This is a fairly well known issue but something that people
> regularly get wrong, too. (Is there maybe a tutorial you did that missed
> giving a pointer on this issue?)
>
> Mark
>
> On Mon, Mar 12, 2018 at 5:21 PM Searle Duay  wrote:
>
> > Good day!
> >
> > I am doing some free energy perturbation to calculate the free energy of
> > binding of an ion to a peptide. For one of my processes, I am slowly
> > turning on the coulombic interactions by an increment of 0.05 lambda,
> > followed by turning on the van der Waals interactions by an increment of
> > 0.05 lambda. This is being done while a pull restraint is present to keep
> > the ion bound to the peptide. Following is a copy of the MDP file of my
> > equilibration run under NPT ensemble:
> >
> > ; Run control
> > integrator   = sd   ; Langevin dynamics
> > tinit= 0
> > dt   = 0.0005
> > nsteps   = 20; 100 ps
> > nstcomm  = 200
> > ; Output control
> > nstxout  = 1000
> > nstvout  = 1000
> > nstfout  = 0
> > nstlog   = 1000
> > nstenergy= 1000
> > nstxout-compressed   = 0
> > ; Neighborsearching and short-range nonbonded interactions
> > cutoff-scheme= Verlet
> > nstlist  = 20
> > ns-type  = grid
> > pbc  = xyz
> > rlist= 1.2
> > ; Electrostatics
> > coulombtype  = pme
> > rcoulomb = 1.2
> > ; van der Waals
> > vdwtype  = Cut-off
> > vdw-modifier = Force-switch
> > rvdw-switch  = 1.0
> > rvdw = 1.2
> > ; Apply long range dispersion corrections for Energy and Pressure
> > DispCorr  = EnerPres
> > ; Spacing for the PME/PPPM FFT grid
> > fourierspacing   = 0.12
> > ; EWALD/PME/PPPM parameters
> > pme-order= 6
> > ewald-rtol   = 1e-06
> > epsilon-surface  = 0
> > ; Temperature coupling
> > ; tcoupl is implicitly handled by the sd integrator
> > tcoupl  = berendsen
> > tc-grps  = PROT   SOL_ION
> > tau-t= 1.01.0
> > ref-t= 300   300
> > ; Pressure coupling is on for NPT
> > pcoupl   = berendsen
> > pcoupltype = isotropic
> > tau-p= 5.0
> > compressibility  = 4.5e-5   4.5e-5
> > ref-p= 1.0  1.0
> > ; Free energy control stuff
> > free-energy  = yes
> > init-lambda-state= 1
> > delta-lambda = 0
> > calc-lambda-neighbors= 1; only immediate neighboring windows
> > ; Vectors of lambda specified here
> > ; Each combination is an index that is retrieved from init_lambda_state
> for
> > each simulation
> > ; init_lambda_state0123456789
> >   10   11   12   13   14   15   16   17   18   19   20   21   22   23
>  24
> >  25   26   27   28   29   30   31   32   33   34   35   36   37   38   39
> >  40   41   42   43   44   45   46   47   48   49   50   51   52   53   54
> >  55   56   57   58   59   60
> > vdw-lambdas  = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10
> 0.15
> > 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85
> 0.90
> > 0.95 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> 1.00
> > 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> > coul-lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
> > 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00
> 1.00
> > 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> 1.00
> > 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> 1.00
> > 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> > ; We are not transforming any bonded or restrained interactions
> > bonded-lambdas   = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > restraint-lambdas= 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> > 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.

Re: [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?

Hi,

Yes, you can specify which energy-group pairs get which tables, and which
do not get any (thus get the normal thing). Did you check out the
documentation yet?

Mark

On Mon, Mar 12, 2018 at 5:30 PM Debdas Dhabal 
wrote:

> Hello everyone,
>
> Could anyone of you help me regarding the aforementioned problem. It would
> be very nice of you.
>
> Thanks in advance.
>
> With regards
> Debdas
>
> On Sat, Mar 10, 2018 at 1:30 PM, Debdas Dhabal 
> wrote:
>
> > Dear Mark,
> >
> > Thanks  so much for your prompt reply. I had gone through that manual and
> > I was able to use two different non-bonded potential for two different
> > energy groups using table potential. But my question is a bit different.
> > May be I was not able to make my question clear. I know the fact that by
> > using table file I can use two different non bonded potential but what I
> > wanted to ask whether it is possible to use table file only for user
> > defined potential and not for which Gromacs already have predefined
> > potential at the same time.
> >
> > Let me make it more clear. I have a system of solute in water. I want to
> > use table file for only solute-water interaction and want to let the
> > Gromacs take LJ potential for water-water interaction (ie. I don't want
> to
> > explicitly supply water-water interaction through Table file). In another
> > way one can ask if I put *"vdwtype=User"* then is it *mandatory* to give
> > non-bonded potential for both solute-water as well as water-water
> > interaction through Table file only, or one can only use Table file for
> > solute-water and Let the Gromacs take its predefined LJ potential form
> for
> > water-water interaction (as in case of vdwtype = Cut-Off case). So
> > basically using Gromacs predefined potential and table potential at the
> > same time.
> >
> > I hope I am able to make my question more clearer than before. Thanks
> > again for your help.
> >
> > With regards
> > Debdas
> >
> > On Sat, Mar 10, 2018 at 7:52 AM, Mark Abraham 
> > wrote:
> >
> >> Hi,
> >>
> >> Yes, if you check out the documentation of tabulated non-bonded
> >> interactions in the reference manual, you will see that you can apply
> >> different tables for particles when drawn from different energy groups.
> >>
> >> Mark
> >>
> >> On Sat, Mar 10, 2018 at 1:06 AM Debdas Dhabal 
> >> wrote:
> >>
> >> > Hello everyone,
> >> >
> >> > This question may be very simple to most of the Gromacs user. I wonder
> >> if
> >> > Gromacs allow us to use both user-defined non-bonded potentials (Table
> >> > potential) as well as Gromacs predefined potential at the same time.
> For
> >> > example, if I have a system with a solute in a solvent and for
> >> > solvent-solvent nonbonded interaction, I want to use Gromacs defined
> LJ
> >> > potential but for solute-solvent nonbonded interaction, I want to use
> a
> >> > custom potential using a Table format. I know that solvent-solvent
> >> > interaction can also be incorporated in the Table file and we can run
> >> > Gromacs successfully, but I want to use Table potential only for which
> >> > Gromacs does not have predefined form.   Is it possible ?. If so, I
> >> would
> >> > be grateful if someone could suggest me to how to do that?.
> >> >
> >> > I will appreciate all your valuable inputs. Thanks so much in advance.
> >> >
> >> > --
> >> > Debdas Dhabal
> >> > Postdoctoral Researcher.
> >> > SEAS, Department of Chemical and Biomolecular Engineering,
> >> > The University of Pennsylvania, Philadelphia, PA 19104, USA.
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at
> >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> > posting!
> >> >
> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
> >> > * For (un)subscribe requests visit
> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> > send a mail to gmx-users-requ...@gromacs.org.
> >> >
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/Support
> >> /Mailing_Lists/GMX-Users_List before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> >
> >
> > --
> > Debdas Dhabal
> > Postdoctoral Researcher.
> > SEAS, Department of Chemical and Biomolecular Engineering,
> > The University of Pennsylvania, Philadelphia, PA 19104, USA.
> >
>
>
>
> --
> Debdas Dhabal
> Postdoctoral Researcher.
> SEAS, Department of Chemical and Biomolecular Engineering,
> The University of Pennsylvania, Philadelphia, PA 19104, USA.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe r

Re: [gmx-users] Problems in putting restraints during free energy perturbation calculations

Hi,

Don't do that. You have charges on atoms that have no VDW, so there is
nothing to stop them flying all over the place and imparting crazy forces
on other atoms that have VDW, etc. Turn the VDW fully on before adding any
charge. This is a fairly well known issue but something that people
regularly get wrong, too. (Is there maybe a tutorial you did that missed
giving a pointer on this issue?)

Mark

On Mon, Mar 12, 2018 at 5:21 PM Searle Duay  wrote:

> Good day!
>
> I am doing some free energy perturbation to calculate the free energy of
> binding of an ion to a peptide. For one of my processes, I am slowly
> turning on the coulombic interactions by an increment of 0.05 lambda,
> followed by turning on the van der Waals interactions by an increment of
> 0.05 lambda. This is being done while a pull restraint is present to keep
> the ion bound to the peptide. Following is a copy of the MDP file of my
> equilibration run under NPT ensemble:
>
> ; Run control
> integrator   = sd   ; Langevin dynamics
> tinit= 0
> dt   = 0.0005
> nsteps   = 20; 100 ps
> nstcomm  = 200
> ; Output control
> nstxout  = 1000
> nstvout  = 1000
> nstfout  = 0
> nstlog   = 1000
> nstenergy= 1000
> nstxout-compressed   = 0
> ; Neighborsearching and short-range nonbonded interactions
> cutoff-scheme= Verlet
> nstlist  = 20
> ns-type  = grid
> pbc  = xyz
> rlist= 1.2
> ; Electrostatics
> coulombtype  = pme
> rcoulomb = 1.2
> ; van der Waals
> vdwtype  = Cut-off
> vdw-modifier = Force-switch
> rvdw-switch  = 1.0
> rvdw = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr  = EnerPres
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing   = 0.12
> ; EWALD/PME/PPPM parameters
> pme-order= 6
> ewald-rtol   = 1e-06
> epsilon-surface  = 0
> ; Temperature coupling
> ; tcoupl is implicitly handled by the sd integrator
> tcoupl  = berendsen
> tc-grps  = PROT   SOL_ION
> tau-t= 1.01.0
> ref-t= 300   300
> ; Pressure coupling is on for NPT
> pcoupl   = berendsen
> pcoupltype = isotropic
> tau-p= 5.0
> compressibility  = 4.5e-5   4.5e-5
> ref-p= 1.0  1.0
> ; Free energy control stuff
> free-energy  = yes
> init-lambda-state= 1
> delta-lambda = 0
> calc-lambda-neighbors= 1; only immediate neighboring windows
> ; Vectors of lambda specified here
> ; Each combination is an index that is retrieved from init_lambda_state for
> each simulation
> ; init_lambda_state0123456789
>   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24
>  25   26   27   28   29   30   31   32   33   34   35   36   37   38   39
>  40   41   42   43   44   45   46   47   48   49   50   51   52   53   54
>  55   56   57   58   59   60
> vdw-lambdas  = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 0.15
> 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90
> 0.95 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> coul-lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
> 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 1.00
> 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> ; We are not transforming any bonded or restrained interactions
> bonded-lambdas   = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> restraint-lambdas= 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> 1.00 1.00 0.95 0.90 0.85 0.80 0.75 0.70 0.65 0.60 0.55 0.50 0.45 0.40 0.35
> 0.30 0.25 0.20 0.15 0.10 0.05 0.00
> ; Masses are not changing (particle identities are the same at lambda = 0
> and lambda = 1)
> mass-lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.0

Re: [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?

2018-03-12 Thread Debdas Dhabal

Hello everyone,

Could anyone of you help me regarding the aforementioned problem. It would
be very nice of you.

Thanks in advance.

With regards
Debdas

On Sat, Mar 10, 2018 at 1:30 PM, Debdas Dhabal 
wrote:

> Dear Mark,
>
> Thanks  so much for your prompt reply. I had gone through that manual and
> I was able to use two different non-bonded potential for two different
> energy groups using table potential. But my question is a bit different.
> May be I was not able to make my question clear. I know the fact that by
> using table file I can use two different non bonded potential but what I
> wanted to ask whether it is possible to use table file only for user
> defined potential and not for which Gromacs already have predefined
> potential at the same time.
>
> Let me make it more clear. I have a system of solute in water. I want to
> use table file for only solute-water interaction and want to let the
> Gromacs take LJ potential for water-water interaction (ie. I don't want to
> explicitly supply water-water interaction through Table file). In another
> way one can ask if I put *"vdwtype=User"* then is it *mandatory* to give
> non-bonded potential for both solute-water as well as water-water
> interaction through Table file only, or one can only use Table file for
> solute-water and Let the Gromacs take its predefined LJ potential form for
> water-water interaction (as in case of vdwtype = Cut-Off case). So
> basically using Gromacs predefined potential and table potential at the
> same time.
>
> I hope I am able to make my question more clearer than before. Thanks
> again for your help.
>
> With regards
> Debdas
>
> On Sat, Mar 10, 2018 at 7:52 AM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> Yes, if you check out the documentation of tabulated non-bonded
>> interactions in the reference manual, you will see that you can apply
>> different tables for particles when drawn from different energy groups.
>>
>> Mark
>>
>> On Sat, Mar 10, 2018 at 1:06 AM Debdas Dhabal 
>> wrote:
>>
>> > Hello everyone,
>> >
>> > This question may be very simple to most of the Gromacs user. I wonder
>> if
>> > Gromacs allow us to use both user-defined non-bonded potentials (Table
>> > potential) as well as Gromacs predefined potential at the same time. For
>> > example, if I have a system with a solute in a solvent and for
>> > solvent-solvent nonbonded interaction, I want to use Gromacs defined LJ
>> > potential but for solute-solvent nonbonded interaction, I want to use a
>> > custom potential using a Table format. I know that solvent-solvent
>> > interaction can also be incorporated in the Table file and we can run
>> > Gromacs successfully, but I want to use Table potential only for which
>> > Gromacs does not have predefined form.   Is it possible ?. If so, I
>> would
>> > be grateful if someone could suggest me to how to do that?.
>> >
>> > I will appreciate all your valuable inputs. Thanks so much in advance.
>> >
>> > --
>> > Debdas Dhabal
>> > Postdoctoral Researcher.
>> > SEAS, Department of Chemical and Biomolecular Engineering,
>> > The University of Pennsylvania, Philadelphia, PA 19104, USA.
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>
> --
> Debdas Dhabal
> Postdoctoral Researcher.
> SEAS, Department of Chemical and Biomolecular Engineering,
> The University of Pennsylvania, Philadelphia, PA 19104, USA.
>



-- 
Debdas Dhabal
Postdoctoral Researcher.
SEAS, Department of Chemical and Biomolecular Engineering,
The University of Pennsylvania, Philadelphia, PA 19104, USA.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

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mail to gmx-users-requ...@gromacs.org.

[gmx-users] Problems in putting restraints during free energy perturbation calculations

2018-03-12 Thread Searle Duay

Good day!

I am doing some free energy perturbation to calculate the free energy of
binding of an ion to a peptide. For one of my processes, I am slowly
turning on the coulombic interactions by an increment of 0.05 lambda,
followed by turning on the van der Waals interactions by an increment of
0.05 lambda. This is being done while a pull restraint is present to keep
the ion bound to the peptide. Following is a copy of the MDP file of my
equilibration run under NPT ensemble:

; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.0005
nsteps   = 20; 100 ps
nstcomm  = 200
; Output control
nstxout  = 1000
nstvout  = 1000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxout-compressed   = 0
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme= Verlet
nstlist  = 20
ns-type  = grid
pbc  = xyz
rlist= 1.2
; Electrostatics
coulombtype  = pme
rcoulomb = 1.2
; van der Waals
vdwtype  = Cut-off
vdw-modifier = Force-switch
rvdw-switch  = 1.0
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; EWALD/PME/PPPM parameters
pme-order= 6
ewald-rtol   = 1e-06
epsilon-surface  = 0
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tcoupl  = berendsen
tc-grps  = PROT   SOL_ION
tau-t= 1.01.0
ref-t= 300   300
; Pressure coupling is on for NPT
pcoupl   = berendsen
pcoupltype = isotropic
tau-p= 5.0
compressibility  = 4.5e-5   4.5e-5
ref-p= 1.0  1.0
; Free energy control stuff
free-energy  = yes
init-lambda-state= 1
delta-lambda = 0
calc-lambda-neighbors= 1; only immediate neighboring windows
; Vectors of lambda specified here
; Each combination is an index that is retrieved from init_lambda_state for
each simulation
; init_lambda_state0123456789
  10   11   12   13   14   15   16   17   18   19   20   21   22   23   24
 25   26   27   28   29   30   31   32   33   34   35   36   37   38   39
 40   41   42   43   44   45   46   47   48   49   50   51   52   53   54
 55   56   57   58   59   60
vdw-lambdas  = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 0.15
0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90
0.95 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
1.00 1.00 1.00 1.00 1.00 1.00 1.00
coul-lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 1.00
1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
1.00 1.00 1.00 1.00 1.00 1.00 1.00
; We are not transforming any bonded or restrained interactions
bonded-lambdas   = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00
restraint-lambdas= 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
1.00 1.00 0.95 0.90 0.85 0.80 0.75 0.70 0.65 0.60 0.55 0.50 0.45 0.40 0.35
0.30 0.25 0.20 0.15 0.10 0.05 0.00
; Masses are not changing (particle identities are the same at lambda = 0
and lambda = 1)
mass-lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Not doing simulated temperting here
temperature-lambdas  = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Options for the decoupling
sc-alpha = 0.5
sc-coul  = no   ; linear in

Re: [gmx-users] rvdw and rcoulomb

2018-03-12 Thread Szilárd Páll

Note that rcoulomb, unlike rvdw, when using a PME long-range
electrostatics, is tunable (together with the PME grid spacing).
--
Szilárd


On Mon, Mar 12, 2018 at 3:43 PM, Justin Lemkul  wrote:
>
>
> On 3/11/18 7:33 PM, Ahmed Mashaly wrote:
>>
>> Dear users,
>> Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind
>> Regards,Ahmed
>>
> These values are a function of the force field and are not freely tunable.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
> mail to gmx-users-requ...@gromacs.org.
-- 
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Re: [gmx-users] Minimal PCI Bandwidth for Gromacs and Infiniband?

2018-03-12 Thread Szilárd Páll

Two things I forgot:

- Ryzen chipsets are limited in the number of PCIE lanes, so if you
plug in a second card (e.g. IB), you'll get x8 on both, which means
GPU transfers will be slower too. Now, this may not be a great issue
if you run multiple ranks per GPU which will provide some
transfer/kernel overlap, boot sooner of later performance will suffer.

- Whether you need IB and which one is worth it vs GbE + RoCE is made
even more tricky by the fact that, GROMACS runs can actually fall on
either on the the bandwidth/latency-bound regime. While as Mark said
for GROMACS performance _mostly_ latency and injection rate what
matters, that's actually only true at high parallelization with small
data/rank hence small message size per rank. Also, newer IB adapters
can get near peak bandwidth already around 4 KB messages size, so if
you don't have too many nodes/MPI ranks, most of your P-to-P traffic
can still benefit from the higher bandwidth of some network -- if that
can be obtained at the relevant messages sizes.
As an example take from the on the previous HPC-AC presentation slide
15 [1] you can see that running the adh benchmark (134k atoms) across
16 nodes you get MPI_Sendrecv 20% <1KB, 15% 1-4KB, 5% 4-16KB, 60%
>16KB. If you take some data from the MVAPICH2 IB point-to-point
benchmarks [2], you can see that e.g. ConnectX-3 get close to peak
bandwidth at messages above 4-8KB, while Connect-IB only above
32-64KB.

[1] 
http://www.hpcadvisorycouncil.com/pdf/GROMACS_Analysis_Intel_E5_2697v3_K40_K80_GPUs.pdf
[2] http://mvapich.cse.ohio-state.edu/performance/pt_to_pt
--
Szilárd


On Mon, Mar 12, 2018 at 4:06 PM, Szilárd Páll  wrote:
> Hi,
>
> Note that it matters a lot how far you want to parallelize and what
> kind of runs would you do? 10 GbE with RoCE may well be enough to
> scale across a couple of such nodes, especially if you can squeeze PME
> into a single node and avoid the MPI collectives across the network.
> You may not even see much difference between, say 10 GbE + RoCE and
> some older IB like CX-3 FDR. However, if you want to run at larger
> strong scale with short time/step, even the P-to-P communication of
> halo-exchange will become a bottleneck on slower networks as
> communications gets purely latency-bound.
>
> I have no data myself nor first-hand experience, but there are some
> results out there, e.g.
> http://www.hpcadvisorycouncil.com/pdf/GROMACS_Analysis_Intel_E5_2697v3_K40_K80_GPUs.pdf
> http://www.hpcadvisorycouncil.com/pdf/GROMACS_Analysis_Intel_E5_2697v3.pdf
>
> Take these with a grain of salt, however, as they seem to show
> different data in places, e.g. slide 10 of the former suggests that
> EDR IB is >3x faster already from 2 nodes with RF, but the latter
> suggests that on 2-4 nodes 10 GbE / 40 GbE is not too awful (though
> compared to EDR IB).
>
> Cheers,
> --
> Szilárd
>
>
> On Mon, Mar 12, 2018 at 9:38 AM, Mark Abraham  
> wrote:
>> Hi,
>>
>> GROMACS doesn't much care about bandwidth, but rather message latency and
>> message injection rate (which in some cases depends on what else is sharing
>> the network). For those, even high quality gigabit ethernet *can* be good
>> enough, so likely any Infiniband product will be just fine. Unfortunately
>> we don't have access to any resource that would permit us to gather
>> comparative data.
>>
>> Mark
>>
>> On Mon, Mar 12, 2018 at 9:09 AM Simon Kit Sang Chu 
>> wrote:
>>
>>> Hi everyone,
>>>
>>> Our group is also interested in purchasing cloud GPU cluster. Amazon only
>>> supplies GPU cluster connected by 10Gb/s bandwidth. I notice this post but
>>> there is no reply by far. It would be nice if someone give any clue.
>>>
>>> Regards,
>>> Simon
>>>
>>> 2018-03-06 1:31 GMT+08:00 Daniel Bauer :
>>>
>>> > Hello,
>>> >
>>> > In our group, we have multiple identical Ryzen 1700x / Nvidia GeForce
>>> > 1080 GTX computing nodes and think about interconnecting them via
>>> > InfiniBands.
>>> >
>>> > Does anyone have Information on what Bandwidth is required by GROMACS
>>> > for communication via InfiniBand (MPI + trajectory writing) and how it
>>> > scales with the number of nodes?
>>> >
>>> > The mainboards we are currently using can only run one PCIe slot with 16
>>> > lanes. When using both PICe slots (GPU+InfiniBand), they will run in
>>> > dual x8 mode (thus bandwidth for both GPU and InfiniBand will be reduced
>>> > to 8 GB/s instead of 16 GB/s). Now we wonder if the reduced bandwidth
>>> > will hurt GROMACS performance due to bottlenecks in GPU/CPU
>>> > communication and/or communication via InfiniBand. If this is the case,
>>> > we might have to upgrade to new mainboards with dual x16 support.
>>> >
>>> >
>>> > Best regards,
>>> >
>>> > Daniel
>>> >
>>> > --
>>> > Daniel Bauer, M.Sc.
>>> >
>>> > TU Darmstadt
>>> > Computational Biology & Simulation
>>> > Schnittspahnstr. 2
>>> > 64287 Darmstadt
>>> > ba...@cbs.tu-darmstadt.de
>>> >
>>> > Don't trust atoms, they make up everything.
>>> >
>>> >
>>> > --
>>> > Gromacs Users mailing li

Re: [gmx-users] Decrease position restraints force constant on the fly

2018-03-12 Thread Dawid das

Hi Zheng,

No, I'm not trying to do steered MD, but rather step by step release my
protein backbone atoms from  position restraints.

Thanks, both of you!

Best wishes,
Dawid

2018-03-12 15:47 GMT+01:00 Zheng Ruan :

> Hi Dawid,
>
> If I understand correctly, you may able to control the restraint using
> plumed. Check the "Moving on a more complex path" in this tutorial (
> https://plumed.github.io/doc-v2.3/user-doc/html/belfast-5.html).
>
> Ruan
>
> On Mon, Mar 12, 2018 at 10:38 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 3/12/18 10:37 AM, Dawid das wrote:
> >
> >> Dear Gromacs Users,
> >>
> >> Is possible to decrease force constant for position restraints as the MD
> >> simulation progresses? For instance I start with 1000 kJ/(mol *nm2) and
> >> after 20 ps I go
> >> to 800 kJ/(mol*nm2), then after 20 ps to 600 kJ/(mol*nm2), etc.?
> >>
> >
> > No, you have to do individual simulations with different force constants.
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalem...@vt.edu | (540) 231-3129
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==
> >
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/Support
> > /Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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[gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?

2018-03-12 Thread Douwe Pollmann

Dear Gromacs users,

I am currently working on a coarse-grained model where I want to fix atoms
(Cb's) on a certain distance from Ca-Ca bonds, so that they can rotate
freely. This freedom will be restricted by a dihedral that determines the
relative orientation between the Cb's.
I am using distance constraints or (non-chemical) bonds between a Cb and
the adjacent Ca's, so that a fixed triangle is formed. I assumed that with
this method the distance from Cb to the Ca-Ca bond should be correct and
that my problem was solved. However, sometimes my simulations crash, and it
appears that both constraint algorithms (LINCS and SHAKE) are not able to
deal with angle constraints / 3 atoms bonded in a triangle.

I came up with two (maybe very strange) idea to solve this problem:
1: There is a third algorithm to solve constraints, called SETTLE, but it
is stated almost everywhere that it is useful for water molecules. Do you
know if it is possible to use SETTLE in other molecules than water, for
example in my system? The Cb would be the "O", and the Ca's the "H's".

2: Is it possible to disable the constraint solver, so that neither Lincs
and Shake are used? I am asking this because someone mentioned that the
solvers are meant to reduce the very fast vibrations of light atoms, so
that a larger mass on my Cb's will also solve the problem.

For the method I want to use I really need the Cb's at fixed distances from
the Ca's and the Ca-Ca bond, but I cannot think of any way without
triangular constraints that fulfils these requirements.

Does any of you know the answers to the two possible solutions, or a way to
fix the distance between Cb and the Ca-Ca bond, while maintaining the free
rotation?

Thank you in advance for any help!

Kind regards,
Douwe Pollmann
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Re: [gmx-users] Minimal PCI Bandwidth for Gromacs and Infiniband?

2018-03-12 Thread Szilárd Páll

Hi,

Note that it matters a lot how far you want to parallelize and what
kind of runs would you do? 10 GbE with RoCE may well be enough to
scale across a couple of such nodes, especially if you can squeeze PME
into a single node and avoid the MPI collectives across the network.
You may not even see much difference between, say 10 GbE + RoCE and
some older IB like CX-3 FDR. However, if you want to run at larger
strong scale with short time/step, even the P-to-P communication of
halo-exchange will become a bottleneck on slower networks as
communications gets purely latency-bound.

I have no data myself nor first-hand experience, but there are some
results out there, e.g.
http://www.hpcadvisorycouncil.com/pdf/GROMACS_Analysis_Intel_E5_2697v3_K40_K80_GPUs.pdf
http://www.hpcadvisorycouncil.com/pdf/GROMACS_Analysis_Intel_E5_2697v3.pdf

Take these with a grain of salt, however, as they seem to show
different data in places, e.g. slide 10 of the former suggests that
EDR IB is >3x faster already from 2 nodes with RF, but the latter
suggests that on 2-4 nodes 10 GbE / 40 GbE is not too awful (though
compared to EDR IB).

Cheers,
--
Szilárd

On Mon, Mar 12, 2018 at 9:38 AM, Mark Abraham  wrote:
> Hi,
>
> GROMACS doesn't much care about bandwidth, but rather message latency and
> message injection rate (which in some cases depends on what else is sharing
> the network). For those, even high quality gigabit ethernet *can* be good
> enough, so likely any Infiniband product will be just fine. Unfortunately
> we don't have access to any resource that would permit us to gather
> comparative data.
>
> Mark
>
> On Mon, Mar 12, 2018 at 9:09 AM Simon Kit Sang Chu 
> wrote:
>
>> Hi everyone,
>>
>> Our group is also interested in purchasing cloud GPU cluster. Amazon only
>> supplies GPU cluster connected by 10Gb/s bandwidth. I notice this post but
>> there is no reply by far. It would be nice if someone give any clue.
>>
>> Regards,
>> Simon
>>
>> 2018-03-06 1:31 GMT+08:00 Daniel Bauer :
>>
>> > Hello,
>> >
>> > In our group, we have multiple identical Ryzen 1700x / Nvidia GeForce
>> > 1080 GTX computing nodes and think about interconnecting them via
>> > InfiniBands.
>> >
>> > Does anyone have Information on what Bandwidth is required by GROMACS
>> > for communication via InfiniBand (MPI + trajectory writing) and how it
>> > scales with the number of nodes?
>> >
>> > The mainboards we are currently using can only run one PCIe slot with 16
>> > lanes. When using both PICe slots (GPU+InfiniBand), they will run in
>> > dual x8 mode (thus bandwidth for both GPU and InfiniBand will be reduced
>> > to 8 GB/s instead of 16 GB/s). Now we wonder if the reduced bandwidth
>> > will hurt GROMACS performance due to bottlenecks in GPU/CPU
>> > communication and/or communication via InfiniBand. If this is the case,
>> > we might have to upgrade to new mainboards with dual x16 support.
>> >
>> >
>> > Best regards,
>> >
>> > Daniel
>> >
>> > --
>> > Daniel Bauer, M.Sc.
>> >
>> > TU Darmstadt
>> > Computational Biology & Simulation
>> > Schnittspahnstr. 2
>> > 64287 Darmstadt
>> > ba...@cbs.tu-darmstadt.de
>> >
>> > Don't trust atoms, they make up everything.
>> >
>> >
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at http://www.gromacs.org/
>> > Support/Mailing_Lists/GMX-Users_List before posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
> --
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>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
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Re: [gmx-users] Decrease position restraints force constant on the fly

2018-03-12 Thread Zheng Ruan

Hi Dawid,

If I understand correctly, you may able to control the restraint using
plumed. Check the "Moving on a more complex path" in this tutorial (
https://plumed.github.io/doc-v2.3/user-doc/html/belfast-5.html).

Ruan

On Mon, Mar 12, 2018 at 10:38 AM, Justin Lemkul  wrote:

>
>
> On 3/12/18 10:37 AM, Dawid das wrote:
>
>> Dear Gromacs Users,
>>
>> Is possible to decrease force constant for position restraints as the MD
>> simulation progresses? For instance I start with 1000 kJ/(mol *nm2) and
>> after 20 ps I go
>> to 800 kJ/(mol*nm2), then after 20 ps to 600 kJ/(mol*nm2), etc.?
>>
>
> No, you have to do individual simulations with different force constants.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
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Re: [gmx-users] Help with interpreting message for fatal error

2018-03-12 Thread Gregory Poon


Hi Viveca,

Could you share more details of your simulations that may shed any 
light?  I assume that you are using parmbsc1 as the DNA forcefield.  Is 
it an "unusual" system?  We (and I am sure others) simulate DNA (± 
ligand) quite a bit and would be as interested in understanding what is 
going wrong here, although I have never encountered what you are observing.


Best wishes,

Gregory


On 3/12/2018 7:42 AM, Viveca Lindahl wrote:

Hi Gregory,

In the sense that I see it happening repeatedly yes :) But I can't
reproduce it very predictably.

After seeing that (for my small system) I get very large box vector
fluctuations using Parrinello-Rahman, my current assumption is that there
are some stability assumptions made by mdrun internally that are being
violated.
I would still be interested in understanding what actually goes wrong
though.

--
Viveca


On Mon, Mar 12, 2018 at 4:49 PM, Gregory Poon  wrote:


Since there hasn't been any response to your question yet, may I ask: is
it reproducible?

Gregory


On 3/11/2018 7:30 AM, Viveca Lindahl wrote:


Hi,

I'm running a simulation of a periodic DNA molecule. After some time I
get,
sometimes the following error message:

---

A list of missing interactions:
   Proper Dih. of   3917 missing  1

Molecule type 'DNA_chain_A'
the first 10 missing interactions, except for exclusions:
   Proper Dih. atoms  414  417  418  421 global   414   417   418
421

---
Program: gmx mdrun, version 2018.1-dev-20180306-33093601f
Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
MPI rank:0 (out of 32)

Fatal error:
1 of the 10381 bonded interactions could not be calculated because some
atoms
involved moved further apart than the multi-body cut-off distance (0.5465
nm)
or the two-body cut-off distance (1.093 nm), see option -rdd, for pairs
and
tabulated bonds also see option -ddcheck

For more information and tips for troubleshooting, please check the
GROMACS
website at https://na01.safelinks.protection.outlook.com/?url=http%3A%
2F%2Fwww.gromacs.org%2FDocumentation%2FErrors&data=02%7C01%
7Cgpoon%40gsu.edu%7C18eac9ccdd4b479d86c708d5875cbb61%7C515ad
73d8d5e4169895c9789dc742a70%7C0%7C0%7C636563754716997653&
sdata=wUdEASAxNIPHNAmQwBO8EO0Ec8EI%2FVdjY7f7i9R0IYc%3D&reserved=0
---
Rank 0 [Sun Mar 11 13:37:32 2018] [c0-0c1s3n0] application called
MPI_Abort(MPI_COMM_WORLD, 1) - process 0
_pmiu_daemon(SIGCHLD): [NID 00076] [c0-0c1s3n0] [Sun Mar 11 13:37:32 2018]
PE RANK 0 exit signal Aborted
[NID 00076] 2018-03-11 13:37:32 Apid 12709959: initiated application
termination
Application 12709959 exit codes: 134
Application 12709959 resources: utime ~1083s, stime ~16s, Rss ~21376,
inblocks ~34261, outblocks ~55016
---> Reached end of run script.


How should I... proceed here? Is my system set up poorly, is it a bug in
mdrun? Suggestions appreciated.

--
Viveca


--

*Gregory M. K. Poon, PhD, RPh*
Associate Professor
Departments of Chemistry and Nutrition | Georgia State University
NSC 414/415/416 | 50 Decatur St. SE, Atlanta, GA 30302
P.O. Box 3965 | Atlanta, GA 30303
Ph (404) 413-5491 | gp...@gsu.edu 

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--

*Gregory M. K. Poon, PhD, RPh*
Associate Professor
Departments of Chemistry and Nutrition | Georgia State University
NSC 414/415/416 | 50 Decatur St. SE, Atlanta, GA 30302
P.O. Box 3965 | Atlanta, GA 30303
Ph (404) 413-5491 | gp...@gsu.edu 

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Re: [gmx-users] Help with interpreting message for fatal error




On 3/12/18 10:42 AM, Viveca Lindahl wrote:

Hi Gregory,

In the sense that I see it happening repeatedly yes :) But I can't
reproduce it very predictably.

After seeing that (for my small system) I get very large box vector
fluctuations using Parrinello-Rahman, my current assumption is that there
are some stability assumptions made by mdrun internally that are being
violated.
I would still be interested in understanding what actually goes wrong
though.


Periodic molecules are usually used in CNT systems or similar, and the 
typical advice is to not apply pressure coupling along the long axis. I 
suspect interactions get lost when the box fluctuates and the domain 
topology does not get updated correctly. Does it work correctly with OpenMP?


-Justin


--
Viveca


On Mon, Mar 12, 2018 at 4:49 PM, Gregory Poon  wrote:


Since there hasn't been any response to your question yet, may I ask: is
it reproducible?

Gregory


On 3/11/2018 7:30 AM, Viveca Lindahl wrote:


Hi,

I'm running a simulation of a periodic DNA molecule. After some time I
get,
sometimes the following error message:

---

A list of missing interactions:
   Proper Dih. of   3917 missing  1

Molecule type 'DNA_chain_A'
the first 10 missing interactions, except for exclusions:
   Proper Dih. atoms  414  417  418  421 global   414   417   418
421

---
Program: gmx mdrun, version 2018.1-dev-20180306-33093601f
Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
MPI rank:0 (out of 32)

Fatal error:
1 of the 10381 bonded interactions could not be calculated because some
atoms
involved moved further apart than the multi-body cut-off distance (0.5465
nm)
or the two-body cut-off distance (1.093 nm), see option -rdd, for pairs
and
tabulated bonds also see option -ddcheck

For more information and tips for troubleshooting, please check the
GROMACS
website at https://na01.safelinks.protection.outlook.com/?url=http%3A%
2F%2Fwww.gromacs.org%2FDocumentation%2FErrors&data=02%7C01%
7Cgpoon%40gsu.edu%7C18eac9ccdd4b479d86c708d5875cbb61%7C515ad
73d8d5e4169895c9789dc742a70%7C0%7C0%7C636563754716997653&
sdata=wUdEASAxNIPHNAmQwBO8EO0Ec8EI%2FVdjY7f7i9R0IYc%3D&reserved=0
---
Rank 0 [Sun Mar 11 13:37:32 2018] [c0-0c1s3n0] application called
MPI_Abort(MPI_COMM_WORLD, 1) - process 0
_pmiu_daemon(SIGCHLD): [NID 00076] [c0-0c1s3n0] [Sun Mar 11 13:37:32 2018]
PE RANK 0 exit signal Aborted
[NID 00076] 2018-03-11 13:37:32 Apid 12709959: initiated application
termination
Application 12709959 exit codes: 134
Application 12709959 resources: utime ~1083s, stime ~16s, Rss ~21376,
inblocks ~34261, outblocks ~55016
---> Reached end of run script.


How should I... proceed here? Is my system set up poorly, is it a bug in
mdrun? Suggestions appreciated.

--
Viveca


--

*Gregory M. K. Poon, PhD, RPh*
Associate Professor
Departments of Chemistry and Nutrition | Georgia State University
NSC 414/415/416 | 50 Decatur St. SE, Atlanta, GA 30302
P.O. Box 3965 | Atlanta, GA 30303
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Re: [gmx-users] -sep option




On 3/10/18 4:52 PM, Mansoureh Shahbazi wrote:

Dear justin,
I want to make pdb files with regular intervals from a long trajectory.
Can you please tell me an example command line using -sep? I want to 
get 100 pdbs from a 100 ns trajectory with 1ns (1000 ps) intervals.




It's much easier with -dump, just loop over the desired time values in 
ps. Using -sep requires either -dt or -skip.


-Justin

Sent from Yahoo Mail on Android 



On Sat, Mar 10, 2018 at 20:56, Justin Lemkul
 wrote:


On 3/10/18 9:18 AM, Mansoureh Shahbazi wrote:
> Dear colleagues, How should I use -sep option to convert a frame
of a trajectory to pdb? Can anyone send me the command line? Thanks


The -sep option is used to write a given interval of a trajectory
into
separate files. If you just want a single frame, you should use -dump
and the corresponding time in ps.

-Justin

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==


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303 Engel Hall
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Blacksburg, VA 24061

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Re: [gmx-users] seeming paradox with gmx wham




On 3/11/18 8:05 PM, Alex wrote:
Just to add to my question... The pull code for the umbrella sampling 
from each of the N configs, as used in Justin's tutorial, is


pull_coord1_type    = umbrella
pull_coord1_geometry    = distance
...
pull_coord1_dim = N N Y

So, in each of the generated pullf and pullx files we sample a flat 
slice at a given Z, and the reported forces and displacements are 
along Z. What appears to be the reaction coordinate in our case is the 
radius from the pore mouth, and one has to sample a set of hemispheres 
from a series of radius values. Is this at all a possibility?




Yes, but not by following the tutorial. You'd need to use 
pull_coord1_dim = Y Y Y to restrict the ions to a given radius around 
the pore itself. As it is, you're probably underestimating entropic 
contributions to the free energy.


-Justin

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Re: [gmx-users] rvdw and rcoulomb




On 3/11/18 7:33 PM, Ahmed Mashaly wrote:

Dear users,
Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind Regards,Ahmed


These values are a function of the force field and are not freely tunable.

-Justin

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Re: [gmx-users] Help with interpreting message for fatal error

2018-03-12 Thread Viveca Lindahl

Hi Gregory,

In the sense that I see it happening repeatedly yes :) But I can't
reproduce it very predictably.

After seeing that (for my small system) I get very large box vector
fluctuations using Parrinello-Rahman, my current assumption is that there
are some stability assumptions made by mdrun internally that are being
violated.
I would still be interested in understanding what actually goes wrong
though.

--
Viveca


On Mon, Mar 12, 2018 at 4:49 PM, Gregory Poon  wrote:

> Since there hasn't been any response to your question yet, may I ask: is
> it reproducible?
>
> Gregory
>
>
> On 3/11/2018 7:30 AM, Viveca Lindahl wrote:
>
>> Hi,
>>
>> I'm running a simulation of a periodic DNA molecule. After some time I
>> get,
>> sometimes the following error message:
>>
>> ---
>>
>> A list of missing interactions:
>>   Proper Dih. of   3917 missing  1
>>
>> Molecule type 'DNA_chain_A'
>> the first 10 missing interactions, except for exclusions:
>>   Proper Dih. atoms  414  417  418  421 global   414   417   418
>> 421
>>
>> ---
>> Program: gmx mdrun, version 2018.1-dev-20180306-33093601f
>> Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
>> MPI rank:0 (out of 32)
>>
>> Fatal error:
>> 1 of the 10381 bonded interactions could not be calculated because some
>> atoms
>> involved moved further apart than the multi-body cut-off distance (0.5465
>> nm)
>> or the two-body cut-off distance (1.093 nm), see option -rdd, for pairs
>> and
>> tabulated bonds also see option -ddcheck
>>
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at https://na01.safelinks.protection.outlook.com/?url=http%3A%
>> 2F%2Fwww.gromacs.org%2FDocumentation%2FErrors&data=02%7C01%
>> 7Cgpoon%40gsu.edu%7C18eac9ccdd4b479d86c708d5875cbb61%7C515ad
>> 73d8d5e4169895c9789dc742a70%7C0%7C0%7C636563754716997653&
>> sdata=wUdEASAxNIPHNAmQwBO8EO0Ec8EI%2FVdjY7f7i9R0IYc%3D&reserved=0
>> ---
>> Rank 0 [Sun Mar 11 13:37:32 2018] [c0-0c1s3n0] application called
>> MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>> _pmiu_daemon(SIGCHLD): [NID 00076] [c0-0c1s3n0] [Sun Mar 11 13:37:32 2018]
>> PE RANK 0 exit signal Aborted
>> [NID 00076] 2018-03-11 13:37:32 Apid 12709959: initiated application
>> termination
>> Application 12709959 exit codes: 134
>> Application 12709959 resources: utime ~1083s, stime ~16s, Rss ~21376,
>> inblocks ~34261, outblocks ~55016
>> ---> Reached end of run script.
>>
>>
>> How should I... proceed here? Is my system set up poorly, is it a bug in
>> mdrun? Suggestions appreciated.
>>
>> --
>> Viveca
>>
> --
>
> *Gregory M. K. Poon, PhD, RPh*
> Associate Professor
> Departments of Chemistry and Nutrition | Georgia State University
> NSC 414/415/416 | 50 Decatur St. SE, Atlanta, GA 30302
> P.O. Box 3965 | Atlanta, GA 30303
> Ph (404) 413-5491 | gp...@gsu.edu 
>
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Re: [gmx-users] NPT equilibration failing at high temperature

On 3/12/18 3:42 AM, Joe Jordan wrote:

You should use the hint in the error message, that the system is not well
equilibrated. Try a shorter time step or a double precision minimization.
Also see
http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group
for info.

A shorter time step is probably the best solution. Such high
temperatures lead to extremely frequent, high-energy collisions between
water and solute (and everything, really) leading to high forces. Most
force fields haven't been validated for use at such temperatures,
because you're well beyond boiling the water at that point.

-Justin

On Mon, Mar 12, 2018 at 7:18 AM, brataraj ghosh
wrote:

Hi
I am trying to simulate a system contains two identical protein chains.
I am equilibrating the system at 7 different temperatures. All the nvt ones
have completed without any errors. 5 npt ones are also completed but in
case of two highest temperatures 679.35 k and 800.0 k it is showing this
following error
"2 particles communicated to PME rank 2 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated."

Any suggestions how to solve this issue?
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Re: [gmx-users] Easiest way to calculate the POTENTIAL ENERGY of a single isolated chain in GROMACS




On 3/12/18 9:37 AM, sanjeet kumar singh ch16d012 wrote:

Hello list,
   Can anyone please tell me about how can i calculate the POTENTIAL
ENERGY of a single isolated chain in the most easiest way in GROMACS.


Generate a topology, .tpr, and use mdrun -rerun to evaluate the energy 
of a given configuration in a non-periodic system.


-Justin

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Re: [gmx-users] Strange jumps in box dimensions




On 3/12/18 10:27 AM, Igor Ariz wrote:

Hi all,

I am simulating a small membrane protein system:

Protein  1 (256 aminoacids)
DPPC    104
SOL    4377
CL    7
NA    1

using CHARMM36m force-field, short cut-offs (0.9 nm) and 
semi-isotropic Berendsen p-coupling.




Short cutoffs can lead to bad lipid properties. There is extensive 
literature on proper cutoff and switching distances for CHARMM lipids.


I am experiencing sudden jumps in box dimensions from [6.52 6.52 6.96] 
to [5.05 5.05 7.72]
in tens of nanoseconds, which take hundreds of nanoseconds to go back 
to the previous box size.




This suggests you have some instability in the system, perhaps void 
space that compresses down.


-Justin

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==

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Re: [gmx-users] Decrease position restraints force constant on the fly




On 3/12/18 10:37 AM, Dawid das wrote:

Dear Gromacs Users,

Is possible to decrease force constant for position restraints as the MD
simulation progresses? For instance I start with 1000 kJ/(mol *nm2) and
after 20 ps I go
to 800 kJ/(mol*nm2), then after 20 ps to 600 kJ/(mol*nm2), etc.?


No, you have to do individual simulations with different force constants.

-Justin

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[gmx-users] Decrease position restraints force constant on the fly

2018-03-12 Thread Dawid das

Dear Gromacs Users,

Is possible to decrease force constant for position restraints as the MD
simulation progresses? For instance I start with 1000 kJ/(mol *nm2) and
after 20 ps I go
to 800 kJ/(mol*nm2), then after 20 ps to 600 kJ/(mol*nm2), etc.?

Best wishes,
Dawid Grabarek
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[gmx-users] Strange jumps in box dimensions

2018-03-12 Thread Igor Ariz


Hi all,

I am simulating a small membrane protein system:

Protein  1 (256 aminoacids)
DPPC    104
SOL    4377
CL    7
NA    1

using CHARMM36m force-field, short cut-offs (0.9 nm) and semi-isotropic 
Berendsen p-coupling.


I am experiencing sudden jumps in box dimensions from [6.52 6.52 6.96] 
to [5.05 5.05 7.72]
in tens of nanoseconds, which take hundreds of nanoseconds to go back to 
the previous box size.


Has anyone ever seen anything similar?

Igor
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Re: [gmx-users] Comm-mode

Thank you very much.

On Mar 12, 2018 14:51, "Justin Lemkul"  wrote:

>
>
> On 3/12/18 9:48 AM, Amin Rouy wrote:
>
>> Ahan, thanks Justin. Is it default in all versions of  Gromacs?
>>
>
> As far as I remember, yes, but don't take my word for it. Look at
> mdout.mdp from grompp - it has the full list of every setting that's being
> used in your simulation (and also the top of md.log, though some of those
> are parsed in ways that make them harder to understand).
>
> -Justin
>
> On Mon, Mar 12, 2018 at 2:44 PM, Justin Lemkul  wrote:
>>
>>
>>> On 3/12/18 9:31 AM, Mark Abraham wrote:
>>>
>>> Hi,

 Very many things are often simplified when you make a tutorial. Those
 .mdp
 files are already complicated enough for a beginner.

 Indeed, and comm-mode = linear is the default behavior, so it works just
>>> fine without bothering the user to think about such abstract concepts :)
>>>
>>> -Justin
>>>
>>>
>>> Mark
>>>
 On Mon, Mar 12, 2018 at 2:26 PM Amin Rouy 
 wrote:

 But, why in some Gromacs tutorial there is no comm-mode used in .mdp
 file,

> for example in 'Lysozyme in water';
>
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
> -tutorials/lysozyme/index.html
>
> On Mon, Mar 12, 2018 at 1:50 PM, Mark Abraham <
> mark.j.abra...@gmail.com>
> wrote:
>
> Hi,
>
>> If you get this wrong, the equipartition of energy is usually broken
>> and
>> the simulation is probably unphysical.
>>
>> Mark
>>
>> On Mon, Mar 12, 2018, 13:47 Amin Rouy  wrote:
>>
>> Dear Justin,
>>
>>> If we do not use comm-mode, which quantity might be changed after
>>> simulations?
>>>
>>> Can we remove center of mass after the simulation done?
>>>
>>> On Sat, Mar 10, 2018 at 6:36 PM, Amin Rouy 
>>>
>>> wrote:
>>
>> thank you so much.
>>>
 On Sat, Mar 10, 2018 at 6:33 PM, Justin Lemkul 

 wrote:
>>>
 On 3/10/18 12:31 PM, Amin Rouy wrote:
>
> Thank you Justin.
>
>> What if we do not know the phase of the final result? of if we are
>>
>> in 2
>
 phase region (gas-liquid)
>>>
 If you're applying PBC you have to use linear as your comm-mode
>>
> (grompp

>>> will fail otherwise, so that's a pretty good hint).
>>>
 -Justin
>
>
> On Sat, Mar 10, 2018 at 6:25 PM, Justin Lemkul 
>
> wrote:

> On 3/10/18 12:17 PM, Amin Rouy wrote:
>>
>>> Dear Gromacs people,
>>>
>>> I have a question please.

 In which condition we must use center of mass removal? Is that
 optional or
 necessary?

 Typically necessary.

 and how to know which mode (linear or angular) is better for our
>>>
>>> simulations?
>>>
 Linear is only for condensed-phase systems, angular is only for

 vacuum
>>>
>> simulations.

> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
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>>>
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>>> -users
>>>
>> or
>>
>> send a mail to gmx-users-requ...@gromacs.org.
>>>

>>> --
>>>
>> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
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Re: [gmx-users] Comm-mode




On 3/12/18 9:48 AM, Amin Rouy wrote:

Ahan, thanks Justin. Is it default in all versions of  Gromacs?


As far as I remember, yes, but don't take my word for it. Look at 
mdout.mdp from grompp - it has the full list of every setting that's 
being used in your simulation (and also the top of md.log, though some 
of those are parsed in ways that make them harder to understand).


-Justin


On Mon, Mar 12, 2018 at 2:44 PM, Justin Lemkul  wrote:



On 3/12/18 9:31 AM, Mark Abraham wrote:


Hi,

Very many things are often simplified when you make a tutorial. Those .mdp
files are already complicated enough for a beginner.


Indeed, and comm-mode = linear is the default behavior, so it works just
fine without bothering the user to think about such abstract concepts :)

-Justin


Mark

On Mon, Mar 12, 2018 at 2:26 PM Amin Rouy  wrote:

But, why in some Gromacs tutorial there is no comm-mode used in .mdp file,

for example in 'Lysozyme in water';


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
-tutorials/lysozyme/index.html

On Mon, Mar 12, 2018 at 1:50 PM, Mark Abraham 
wrote:

Hi,

If you get this wrong, the equipartition of energy is usually broken and
the simulation is probably unphysical.

Mark

On Mon, Mar 12, 2018, 13:47 Amin Rouy  wrote:

Dear Justin,

If we do not use comm-mode, which quantity might be changed after
simulations?

Can we remove center of mass after the simulation done?

On Sat, Mar 10, 2018 at 6:36 PM, Amin Rouy 


wrote:


thank you so much.

On Sat, Mar 10, 2018 at 6:33 PM, Justin Lemkul 


wrote:

On 3/10/18 12:31 PM, Amin Rouy wrote:

Thank you Justin.

What if we do not know the phase of the final result? of if we are


in 2

phase region (gas-liquid)

If you're applying PBC you have to use linear as your comm-mode

(grompp

will fail otherwise, so that's a pretty good hint).

-Justin


On Sat, Mar 10, 2018 at 6:25 PM, Justin Lemkul 


wrote:

On 3/10/18 12:17 PM, Amin Rouy wrote:

Dear Gromacs people,


I have a question please.

In which condition we must use center of mass removal? Is that
optional or
necessary?

Typically necessary.


and how to know which mode (linear or angular) is better for our

simulations?

Linear is only for condensed-phase systems, angular is only for


vacuum

simulations.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Virginia Tech Department of Biochemistry

303 Engel Hall
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jalem...@vt.edu | (540) 231-3129
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Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 2

Re: [gmx-users] Comm-mode

Ahan, thanks Justin. Is it default in all versions of  Gromacs?

On Mon, Mar 12, 2018 at 2:44 PM, Justin Lemkul  wrote:

>
>
> On 3/12/18 9:31 AM, Mark Abraham wrote:
>
>> Hi,
>>
>> Very many things are often simplified when you make a tutorial. Those .mdp
>> files are already complicated enough for a beginner.
>>
>
> Indeed, and comm-mode = linear is the default behavior, so it works just
> fine without bothering the user to think about such abstract concepts :)
>
> -Justin
>
>
> Mark
>>
>> On Mon, Mar 12, 2018 at 2:26 PM Amin Rouy  wrote:
>>
>> But, why in some Gromacs tutorial there is no comm-mode used in .mdp file,
>>> for example in 'Lysozyme in water';
>>>
>>>
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
>>> -tutorials/lysozyme/index.html
>>>
>>> On Mon, Mar 12, 2018 at 1:50 PM, Mark Abraham 
>>> wrote:
>>>
>>> Hi,

 If you get this wrong, the equipartition of energy is usually broken and
 the simulation is probably unphysical.

 Mark

 On Mon, Mar 12, 2018, 13:47 Amin Rouy  wrote:

 Dear Justin,
>
> If we do not use comm-mode, which quantity might be changed after
> simulations?
>
> Can we remove center of mass after the simulation done?
>
> On Sat, Mar 10, 2018 at 6:36 PM, Amin Rouy 
>
 wrote:

> thank you so much.
>>
>> On Sat, Mar 10, 2018 at 6:33 PM, Justin Lemkul 
>>
> wrote:

>
>>> On 3/10/18 12:31 PM, Amin Rouy wrote:
>>>
>>> Thank you Justin.
 What if we do not know the phase of the final result? of if we are

>>> in 2

> phase region (gas-liquid)

 If you're applying PBC you have to use linear as your comm-mode
>>>
>> (grompp

> will fail otherwise, so that's a pretty good hint).
>>>
>>> -Justin
>>>
>>>
>>> On Sat, Mar 10, 2018 at 6:25 PM, Justin Lemkul 
>>>
>> wrote:

>
 On 3/10/18 12:17 PM, Amin Rouy wrote:
>
> Dear Gromacs people,
>
>> I have a question please.
>>
>> In which condition we must use center of mass removal? Is that
>> optional or
>> necessary?
>>
>> Typically necessary.
>>
> and how to know which mode (linear or angular) is better for our
>
> simulations?
>>
>> Linear is only for condensed-phase systems, angular is only for
>>
> vacuum
>
>> simulations.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
>
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>
 or

> send a mail to gmx-users-requ...@gromacs.org.
>
>
> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
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>>>
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>>>
>> or
>>>
 send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
>> --
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 * Please search the a

Re: [gmx-users] Comm-mode




On 3/12/18 9:31 AM, Mark Abraham wrote:

Hi,

Very many things are often simplified when you make a tutorial. Those .mdp
files are already complicated enough for a beginner.


Indeed, and comm-mode = linear is the default behavior, so it works just 
fine without bothering the user to think about such abstract concepts :)


-Justin


Mark

On Mon, Mar 12, 2018 at 2:26 PM Amin Rouy  wrote:


But, why in some Gromacs tutorial there is no comm-mode used in .mdp file,
for example in 'Lysozyme in water';


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html

On Mon, Mar 12, 2018 at 1:50 PM, Mark Abraham 
wrote:


Hi,

If you get this wrong, the equipartition of energy is usually broken and
the simulation is probably unphysical.

Mark

On Mon, Mar 12, 2018, 13:47 Amin Rouy  wrote:


Dear Justin,

If we do not use comm-mode, which quantity might be changed after
simulations?

Can we remove center of mass after the simulation done?

On Sat, Mar 10, 2018 at 6:36 PM, Amin Rouy 

wrote:

thank you so much.

On Sat, Mar 10, 2018 at 6:33 PM, Justin Lemkul 

wrote:


On 3/10/18 12:31 PM, Amin Rouy wrote:


Thank you Justin.
What if we do not know the phase of the final result? of if we are

in 2

phase region (gas-liquid)


If you're applying PBC you have to use linear as your comm-mode

(grompp

will fail otherwise, so that's a pretty good hint).

-Justin


On Sat, Mar 10, 2018 at 6:25 PM, Justin Lemkul 

wrote:



On 3/10/18 12:17 PM, Amin Rouy wrote:

Dear Gromacs people,

I have a question please.

In which condition we must use center of mass removal? Is that
optional or
necessary?

Typically necessary.

and how to know which mode (linear or angular) is better for our


simulations?

Linear is only for condensed-phase systems, angular is only for

vacuum

simulations.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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303 Engel Hall
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Blacksburg, VA 24061

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mail to gmx-u

[gmx-users] Easiest way to calculate the POTENTIAL ENERGY of a single isolated chain in GROMACS

2018-03-12 Thread sanjeet kumar singh ch16d012

Hello list,
  Can anyone please tell me about how can i calculate the POTENTIAL
ENERGY of a single isolated chain in the most easiest way in GROMACS.

Cheers,
SK
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[gmx-users] gmx potential calculation with one sodium ion at the center of box

2018-03-12 Thread 이연경


Dear Gromacs users, 

I’m testing a simple system that has one sodium ion to check electric field. 
(NVE simulation)
 
I used gmx potential- to check electric field.

According to gromacs manual 5.0.4 (p.8), ‘the potential of an electronic charge 
at distance of 1nm equals f ~140 units ~ 1.4V.’

I expected the result graphs would represent gaussian form with the highest 
value of 1.4V/nm, but it only calculated upper side of box from where the 
sodium ion was and the highest value was 0.8V/nm. ( linear graph with minus 
slope ) (x axis is BOX(nm) )

Why does gromacs potential not calculate down side of the sodium ion? And why 
was the value different from that of the manual?
 
I’m waiting for your answer.
 
Thanks for your time :)
 
Best regards,

 YK Lee
 
 
 
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Re: [gmx-users] Comm-mode

Hi,

Very many things are often simplified when you make a tutorial. Those .mdp
files are already complicated enough for a beginner.

Mark

On Mon, Mar 12, 2018 at 2:26 PM Amin Rouy  wrote:

> But, why in some Gromacs tutorial there is no comm-mode used in .mdp file,
> for example in 'Lysozyme in water';
>
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html
>
> On Mon, Mar 12, 2018 at 1:50 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > If you get this wrong, the equipartition of energy is usually broken and
> > the simulation is probably unphysical.
> >
> > Mark
> >
> > On Mon, Mar 12, 2018, 13:47 Amin Rouy  wrote:
> >
> > > Dear Justin,
> > >
> > > If we do not use comm-mode, which quantity might be changed after
> > > simulations?
> > >
> > > Can we remove center of mass after the simulation done?
> > >
> > > On Sat, Mar 10, 2018 at 6:36 PM, Amin Rouy 
> > wrote:
> > >
> > > > thank you so much.
> > > >
> > > > On Sat, Mar 10, 2018 at 6:33 PM, Justin Lemkul 
> > wrote:
> > > >
> > > >>
> > > >>
> > > >> On 3/10/18 12:31 PM, Amin Rouy wrote:
> > > >>
> > > >>> Thank you Justin.
> > > >>> What if we do not know the phase of the final result? of if we are
> > in 2
> > > >>> phase region (gas-liquid)
> > > >>>
> > > >>
> > > >> If you're applying PBC you have to use linear as your comm-mode
> > (grompp
> > > >> will fail otherwise, so that's a pretty good hint).
> > > >>
> > > >> -Justin
> > > >>
> > > >>
> > > >> On Sat, Mar 10, 2018 at 6:25 PM, Justin Lemkul 
> > wrote:
> > > >>>
> > > >>>
> > >  On 3/10/18 12:17 PM, Amin Rouy wrote:
> > > 
> > >  Dear Gromacs people,
> > > >
> > > > I have a question please.
> > > >
> > > > In which condition we must use center of mass removal? Is that
> > > > optional or
> > > > necessary?
> > > >
> > > > Typically necessary.
> > > 
> > >  and how to know which mode (linear or angular) is better for our
> > > 
> > > > simulations?
> > > >
> > > > Linear is only for condensed-phase systems, angular is only for
> > > vacuum
> > >  simulations.
> > > 
> > >  -Justin
> > > 
> > >  --
> > >  ==
> > > 
> > >  Justin A. Lemkul, Ph.D.
> > >  Assistant Professor
> > >  Virginia Tech Department of Biochemistry
> > > 
> > >  303 Engel Hall
> > >  340 West Campus Dr.
> > >  Blacksburg, VA 24061
> > > 
> > >  jalem...@vt.edu | (540) 231-3129
> > >  http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > > 
> > >  ==
> > > 
> > >  --
> > >  Gromacs Users mailing list
> > > 
> > >  * Please search the archive at http://www.gromacs.org/Support
> > >  /Mailing_Lists/GMX-Users_List before posting!
> > > 
> > >  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > 
> > >  * For (un)subscribe requests visit
> > > 
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > >  send a mail to gmx-users-requ...@gromacs.org.
> > > 
> > > 
> > > >> --
> > > >> ==
> > > >>
> > > >> Justin A. Lemkul, Ph.D.
> > > >> Assistant Professor
> > > >> Virginia Tech Department of Biochemistry
> > > >>
> > > >> 303 Engel Hall
> > > >> 340 West Campus Dr.
> > > >> Blacksburg, VA 24061
> > > >>
> > > >> jalem...@vt.edu | (540) 231-3129
> > > >> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > > >>
> > > >> ==
> > > >>
> > > >> --
> > > >> Gromacs Users mailing list
> > > >>
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> > > >> /Mailing_Lists/GMX-Users_List before posting!
> > > >>
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> > > >>
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> or
> > > >> send a mail to gmx-users-requ...@gromacs.org.
> > > >>
> > > >
> > > >
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Re: [gmx-users] Comm-mode

But, why in some Gromacs tutorial there is no comm-mode used in .mdp file,
for example in 'Lysozyme in water';

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html

On Mon, Mar 12, 2018 at 1:50 PM, Mark Abraham 
wrote:

> Hi,
>
> If you get this wrong, the equipartition of energy is usually broken and
> the simulation is probably unphysical.
>
> Mark
>
> On Mon, Mar 12, 2018, 13:47 Amin Rouy  wrote:
>
> > Dear Justin,
> >
> > If we do not use comm-mode, which quantity might be changed after
> > simulations?
> >
> > Can we remove center of mass after the simulation done?
> >
> > On Sat, Mar 10, 2018 at 6:36 PM, Amin Rouy 
> wrote:
> >
> > > thank you so much.
> > >
> > > On Sat, Mar 10, 2018 at 6:33 PM, Justin Lemkul 
> wrote:
> > >
> > >>
> > >>
> > >> On 3/10/18 12:31 PM, Amin Rouy wrote:
> > >>
> > >>> Thank you Justin.
> > >>> What if we do not know the phase of the final result? of if we are
> in 2
> > >>> phase region (gas-liquid)
> > >>>
> > >>
> > >> If you're applying PBC you have to use linear as your comm-mode
> (grompp
> > >> will fail otherwise, so that's a pretty good hint).
> > >>
> > >> -Justin
> > >>
> > >>
> > >> On Sat, Mar 10, 2018 at 6:25 PM, Justin Lemkul 
> wrote:
> > >>>
> > >>>
> >  On 3/10/18 12:17 PM, Amin Rouy wrote:
> > 
> >  Dear Gromacs people,
> > >
> > > I have a question please.
> > >
> > > In which condition we must use center of mass removal? Is that
> > > optional or
> > > necessary?
> > >
> > > Typically necessary.
> > 
> >  and how to know which mode (linear or angular) is better for our
> > 
> > > simulations?
> > >
> > > Linear is only for condensed-phase systems, angular is only for
> > vacuum
> >  simulations.
> > 
> >  -Justin
> > 
> >  --
> >  ==
> > 
> >  Justin A. Lemkul, Ph.D.
> >  Assistant Professor
> >  Virginia Tech Department of Biochemistry
> > 
> >  303 Engel Hall
> >  340 West Campus Dr.
> >  Blacksburg, VA 24061
> > 
> >  jalem...@vt.edu | (540) 231-3129
> >  http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > 
> >  ==
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> > >> Assistant Professor
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> > >>
> > >> 303 Engel Hall
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Re: [gmx-users] Comm-mode

Hi,

If you get this wrong, the equipartition of energy is usually broken and
the simulation is probably unphysical.

Mark

On Mon, Mar 12, 2018, 13:47 Amin Rouy  wrote:

> Dear Justin,
>
> If we do not use comm-mode, which quantity might be changed after
> simulations?
>
> Can we remove center of mass after the simulation done?
>
> On Sat, Mar 10, 2018 at 6:36 PM, Amin Rouy  wrote:
>
> > thank you so much.
> >
> > On Sat, Mar 10, 2018 at 6:33 PM, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 3/10/18 12:31 PM, Amin Rouy wrote:
> >>
> >>> Thank you Justin.
> >>> What if we do not know the phase of the final result? of if we are in 2
> >>> phase region (gas-liquid)
> >>>
> >>
> >> If you're applying PBC you have to use linear as your comm-mode (grompp
> >> will fail otherwise, so that's a pretty good hint).
> >>
> >> -Justin
> >>
> >>
> >> On Sat, Mar 10, 2018 at 6:25 PM, Justin Lemkul  wrote:
> >>>
> >>>
>  On 3/10/18 12:17 PM, Amin Rouy wrote:
> 
>  Dear Gromacs people,
> >
> > I have a question please.
> >
> > In which condition we must use center of mass removal? Is that
> > optional or
> > necessary?
> >
> > Typically necessary.
> 
>  and how to know which mode (linear or angular) is better for our
> 
> > simulations?
> >
> > Linear is only for condensed-phase systems, angular is only for
> vacuum
>  simulations.
> 
>  -Justin
> 
>  --
>  ==
> 
>  Justin A. Lemkul, Ph.D.
>  Assistant Professor
>  Virginia Tech Department of Biochemistry
> 
>  303 Engel Hall
>  340 West Campus Dr.
>  Blacksburg, VA 24061
> 
>  jalem...@vt.edu | (540) 231-3129
>  http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> 
>  ==
> 
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> 
> 
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Virginia Tech Department of Biochemistry
> >>
> >> 303 Engel Hall
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >>
> >> ==
> >>
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Re: [gmx-users] Help with interpreting message for fatal error

2018-03-12 Thread Gregory Poon

Since there hasn't been any response to your question yet, may I ask: is 
it reproducible?


Gregory


On 3/11/2018 7:30 AM, Viveca Lindahl wrote:

Hi,

I'm running a simulation of a periodic DNA molecule. After some time I get,
sometimes the following error message:

---

A list of missing interactions:
  Proper Dih. of   3917 missing  1

Molecule type 'DNA_chain_A'
the first 10 missing interactions, except for exclusions:
  Proper Dih. atoms  414  417  418  421 global   414   417   418
421

---
Program: gmx mdrun, version 2018.1-dev-20180306-33093601f
Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
MPI rank:0 (out of 32)

Fatal error:
1 of the 10381 bonded interactions could not be calculated because some
atoms
involved moved further apart than the multi-body cut-off distance (0.5465
nm)
or the two-body cut-off distance (1.093 nm), see option -rdd, for pairs and
tabulated bonds also see option -ddcheck

For more information and tips for troubleshooting, please check the GROMACS
website at 
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FErrors&data=02%7C01%7Cgpoon%40gsu.edu%7C18eac9ccdd4b479d86c708d5875cbb61%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C636563754716997653&sdata=wUdEASAxNIPHNAmQwBO8EO0Ec8EI%2FVdjY7f7i9R0IYc%3D&reserved=0
---
Rank 0 [Sun Mar 11 13:37:32 2018] [c0-0c1s3n0] application called
MPI_Abort(MPI_COMM_WORLD, 1) - process 0
_pmiu_daemon(SIGCHLD): [NID 00076] [c0-0c1s3n0] [Sun Mar 11 13:37:32 2018]
PE RANK 0 exit signal Aborted
[NID 00076] 2018-03-11 13:37:32 Apid 12709959: initiated application
termination
Application 12709959 exit codes: 134
Application 12709959 resources: utime ~1083s, stime ~16s, Rss ~21376,
inblocks ~34261, outblocks ~55016
---> Reached end of run script.


How should I... proceed here? Is my system set up poorly, is it a bug in
mdrun? Suggestions appreciated.

--
Viveca

--

*Gregory M. K. Poon, PhD, RPh*
Associate Professor
Departments of Chemistry and Nutrition | Georgia State University
NSC 414/415/416 | 50 Decatur St. SE, Atlanta, GA 30302
P.O. Box 3965 | Atlanta, GA 30303
Ph (404) 413-5491 | gp...@gsu.edu 

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Re: [gmx-users] Comm-mode

Dear Justin,

If we do not use comm-mode, which quantity might be changed after
simulations?

Can we remove center of mass after the simulation done?

On Sat, Mar 10, 2018 at 6:36 PM, Amin Rouy  wrote:

> thank you so much.
>
> On Sat, Mar 10, 2018 at 6:33 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 3/10/18 12:31 PM, Amin Rouy wrote:
>>
>>> Thank you Justin.
>>> What if we do not know the phase of the final result? of if we are in 2
>>> phase region (gas-liquid)
>>>
>>
>> If you're applying PBC you have to use linear as your comm-mode (grompp
>> will fail otherwise, so that's a pretty good hint).
>>
>> -Justin
>>
>>
>> On Sat, Mar 10, 2018 at 6:25 PM, Justin Lemkul  wrote:
>>>
>>>
 On 3/10/18 12:17 PM, Amin Rouy wrote:

 Dear Gromacs people,
>
> I have a question please.
>
> In which condition we must use center of mass removal? Is that
> optional or
> necessary?
>
> Typically necessary.

 and how to know which mode (linear or angular) is better for our

> simulations?
>
> Linear is only for condensed-phase systems, angular is only for vacuum
 simulations.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Assistant Professor
 Virginia Tech Department of Biochemistry

 303 Engel Hall
 340 West Campus Dr.
 Blacksburg, VA 24061

 jalem...@vt.edu | (540) 231-3129
 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

 ==

 --
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 * Please search the archive at http://www.gromacs.org/Support
 /Mailing_Lists/GMX-Users_List before posting!

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 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.

>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalem...@vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
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>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] How to define ligand / metal atoms in gbsa.itp file of a force field for implicit MD??

Hi,

On Mon, Mar 12, 2018 at 10:11 AM Vishwambhar Bhandare 
wrote:

> Dear users,
>
> I want to perform implicit simulation for a protein-ligand complex.
> for a protein alone, implicit works fine, but for ligand atoms it shows
> error as copied below,
>
> Setting gen_seed to -1914387900
> Velocities were taken from a Maxwell distribution at 300 K
> GB parameter(s) missing or negative for atom type 'N3'
> GB parameter(s) missing or negative for atom type 'H'
> GB parameter(s) missing or negative for atom type 'CT'
> GB parameter(s) missing or negative for atom type 'HP'
> GB parameter(s) missing or negative for atom type 'HC'
> GB parameter(s) missing or negative for atom type 'H1'
> GB parameter(s) missing or negative for atom type 'S'
> GB parameter(s) missing or negative for atom type 'C'
> GB parameter(s) missing or negative for atom type 'O'
> GB parameter(s) missing or negative for atom type 'OH'
> GB parameter(s) missing or negative for atom type 'HO'
> GB parameter(s) missing or negative for atom type 'H5'
> GB parameter(s) missing or negative for atom type 'H4'
> GB parameter(s) missing or negative for atom type 'HA'
> GB parameter(s) missing or negative for atom type 'MG'
> GB parameter(s) missing or negative for atom type 'P'
> GB parameter(s) missing or negative for atom type 'OS'
> GB parameter(s) missing or negative for atom type 'H2'
> GB parameter(s) missing or negative for atom type 'c1'
>
> Program: gmx grompp, version 2016.4
>
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1296)
> Fatal error:
> Can't do GB electrostatics; the implicit_genborn_params section of the
> forcefield is missing parameters for 19 atomtypes or they might be
> negative.
>
>
> How can I get the parameters defined in gbsa.itp file..???
>

The general answer to this is "develop the parameters using a method
consistent with the way the rest of the parameters were developed" which
generally means you need to read and understand how those were developed,
and use the same tools to fill gaps. In many cases you can probably define
radii by analogy between the atom types, and how buried the ligand is, but
that's a judgement you need to make as part of developing the description
of your system.

Mark


> --
> Dr. Vishwambhar Vishnu Bhandare
> Post Doctoral Fellow
> Department of Biosciences and Bioengineering
> Indian Institute of Technology
> Bombay-400076
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[gmx-users] Fw: -sep option

2018-03-12 Thread Mansoureh Shahbazi

Sent from Yahoo Mail on Android 

   - Forwarded Message - From: "Mansoureh Shahbazi" 
 To: "gmx-us...@gromacs.org" 
, "Justin Lemkul"  Cc:  Sent: Sun, Mar 
11, 2018 at 1:22 Subject: Re: [gmx-users] -sep option  Dear justin, I want to 
make pdb files with regular intervals from a long trajectory.Can you please 
tell me an example command line using -sep? I want to get 100 pdbs from a 100 
ns trajectory with 1ns (1000 ps) intervals. 

Sent from Yahoo Mail on Android 

  On Sat, Mar 10, 2018 at 20:56, Justin Lemkul wrote:   

On 3/10/18 9:18 AM, Mansoureh Shahbazi wrote:
> Dear colleagues, How should I use -sep option to convert a frame of a 
> trajectory to pdb? Can anyone send me the command line? Thanks

The -sep option is used to write a given interval of a trajectory into 
separate files. If you just want a single frame, you should use -dump 
and the corresponding time in ps.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] How to define ligand / metal atoms in gbsa.itp file of a force field for implicit MD??

2018-03-12 Thread Vishwambhar Bhandare

Dear users,

I want to perform implicit simulation for a protein-ligand complex.
for a protein alone, implicit works fine, but for ligand atoms it shows
error as copied below,

Setting gen_seed to -1914387900
Velocities were taken from a Maxwell distribution at 300 K
GB parameter(s) missing or negative for atom type 'N3'
GB parameter(s) missing or negative for atom type 'H'
GB parameter(s) missing or negative for atom type 'CT'
GB parameter(s) missing or negative for atom type 'HP'
GB parameter(s) missing or negative for atom type 'HC'
GB parameter(s) missing or negative for atom type 'H1'
GB parameter(s) missing or negative for atom type 'S'
GB parameter(s) missing or negative for atom type 'C'
GB parameter(s) missing or negative for atom type 'O'
GB parameter(s) missing or negative for atom type 'OH'
GB parameter(s) missing or negative for atom type 'HO'
GB parameter(s) missing or negative for atom type 'H5'
GB parameter(s) missing or negative for atom type 'H4'
GB parameter(s) missing or negative for atom type 'HA'
GB parameter(s) missing or negative for atom type 'MG'
GB parameter(s) missing or negative for atom type 'P'
GB parameter(s) missing or negative for atom type 'OS'
GB parameter(s) missing or negative for atom type 'H2'
GB parameter(s) missing or negative for atom type 'c1'

Program: gmx grompp, version 2016.4

Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1296)
Fatal error:
Can't do GB electrostatics; the implicit_genborn_params section of the
forcefield is missing parameters for 19 atomtypes or they might be negative.


How can I get the parameters defined in gbsa.itp file..???


-- 
Dr. Vishwambhar Vishnu Bhandare
Post Doctoral Fellow
Department of Biosciences and Bioengineering
Indian Institute of Technology
Bombay-400076
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Re: [gmx-users] Minimal PCI Bandwidth for Gromacs and Infiniband?