Re: [gmx-users] GMX 2018 and 'distance' pull

[Alex]

What I meant is each of those files now has two columns, the first of 
which is of course time. What the second column is, especially for 
pullf, is a mystery to me. The total radial force? I wish someone who 
wrote the new pull code would clarify, because the result of wham now 
looks rather strange -- a long (1.5 nm!) hydration barrier for the ion. 
Makes little physical sense and very different from the bias along Z case.


I am guessing that the sampling of 1 ns per hemispherical slice is far 
from sufficient to probe that space... Just looked at one of the 
trajectories there -- the ion is nowhere near moving around the entire 
slice.


Alex


On 3/13/2018 10:27 AM, Justin Lemkul wrote:



On 3/13/18 10:32 AM, Alex wrote:
It appears that things have improved... I am just glancing and pullf 
and pullx data from the first sample config and both contain only one 
value, even though we set dim to 3D. Does this make sense?




I haven't used the 2018 pull code yet. Presumably this is correct, 
just the distance rather than all its components, though that would be 
a change from previous versions.


-Justin


Thanks,

Alex

On 3/13/2018 8:18 AM, Justin Lemkul wrote:



On 3/13/18 10:17 AM, Alex wrote:

Justin,
You may have a situation that requires manual assignment of 
pull_group1_pbcatom1, as the automatic choice of 


Sorry, that should be pull_group1_pbcatom. Must remind myself not 
to email before coffee...



Did you mean pull_group2_pbcatom? In my case:

pull_group1_name    = K
pull_group2_name    = CNT

The language for 5.1 pull is (you be the judge on how clear it is):

pull-group1-pbcatom 



   (0) The reference atom for the treatment of periodic boundary
   conditions inside the group (this has no effect on the treatment of
   the pbc between groups). This option is only important when the
   diameter of the pull group is larger than half the shortest box
   vector. For determining the COM, all atoms in the group are put at
   their periodic image which is closest topull-group1-pbcatom
. 


   A value of 0 means that the middle atom (number wise) is used. This
   parameter is not used withpull-group1-geometrycylinder. A value of
   -1 turns on cosine weighting, which is useful for a group of
   molecules in a periodic system,/e.g./a water slab (see Engin et al.
   J. Chem. Phys. B 2010).

Indeed, my group2 is a membrane that is wider than the shortest 
half-box. I am assuming it would be a single atom belonging to the 
pore region...




Yes, pull_group2_pbcatom, not 1.

-Justin


Thanks,

Alex








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[gmx-users] GROMACS 5.1.4 and dssp 2.2.1

[Simon Kit Sang Chu]

Hi everyone.

I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1. It returned
an error:


Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option.


I can run mkdssp and it is placed in bin. Is it a compatibility problem
here?

Thanks in advance.

Regards.
Simon
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Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

[João Henriques]

Also, if you're exporting DSSP="/.../dssp" and your bin contains mkdssp and
not dssp, then that's going to fail for obvious reasons. Either export
DSSP="/.../mkdssp"
or create a link to mkdssp within the same directory with the name "dssp"
(ln -s mkdssp dssp). Export and executable name must match.

J

On Tue, Mar 13, 2018 at 8:58 AM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> "Fatal error: Failed to execute command: Try specifying your dssp version
> with the -ver option."
>
> Did you follow the error message suggestion? With DSSP 2.2.1 you need to
> set "-ver 2" on your gmx do_dssp command.
>
> J
>
> On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu <
> simoncks1...@gmail.com> wrote:
>
>> Hi everyone.
>>
>> I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1. It returned
>> an error:
>>
>>
>> Fatal error:
>> Failed to execute command: Try specifying your dssp version with the -ver
>> option.
>>
>>
>> I can run mkdssp and it is placed in bin. Is it a compatibility problem
>> here?
>>
>> Thanks in advance.
>>
>> Regards.
>> Simon
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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)

[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] computation/memory modifications

[Mahmood Naderan]

No idea? Any feedback is appreciated.


Regards,
Mahmood 

On Friday, March 9, 2018, 9:47:33 PM GMT+3:30, Mahmood Naderan 
 wrote:  
 
 Hi,
I want to do some tests on the lysozyme tutorial. Assume that the tutorial with 
the default parameters which is run for 10ps, takes X seconds wall clock time. 
If I want to increase the wall clock time, I can simply run for 100ps. However, 
that is not what I want.
I want to increase the amount of computation for every step, e.g. 1ps. 
Therefore I want another run for 10ps which takes Y seconds wall clock time 
where Y>X. I also want to increase the memory usage for each step compared to 
the default values in the tutorial.
May I know which parameters are chosen for those purposes?

Regards,
Mahmood  
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[gmx-users] Error with CHARMM36 force field

[laurenmr]

Hi Gromacs Users,

I have downloaded the latest version of the CHARMM36M force field. My 
aim is to compare a simulation using CHARMM36M and CHARMM36. In the 
forcefield.itp there is an 'if' statement allowing the user to switch to 
the old CHARMM36 force field by directing to the old cmap itp:


; Allow the user to specify CHARMM36 parameters, instead
; Default behavior is to use CHARMM36m
#ifdef USE_OLD_C36
#include "old_c36_cmap.itp"
#else
#include "cmap.itp"
#endif

However, when I include "define = -DUSE_OLD_C36" in my .mdp file I 
receive this error at the grompp command:


Fatal error:
An input file contains a line longer than 4095 characters, while the 
buffer passed to fgets2 has size 4095. The line starts with: 'C NH1 CT1 
C NH1 1 24'


Could anyone suggest a way around this or should I download an older 
version of CHARMM36 (before CHARMM36M)?


Thanks in advance for the help!

Lauren


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[gmx-users] GMX 2018 and 'distance' pull

[Alex]

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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Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

[João Henriques]

"Fatal error: Failed to execute command: Try specifying your dssp version
with the -ver option."

Did you follow the error message suggestion? With DSSP 2.2.1 you need to
set "-ver 2" on your gmx do_dssp command.

J

On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu 
wrote:

> Hi everyone.
>
> I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1. It returned
> an error:
>
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the -ver
> option.
>
>
> I can run mkdssp and it is placed in bin. Is it a compatibility problem
> here?
>
> Thanks in advance.
>
> Regards.
> Simon
> --
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Re: [gmx-users] Mentioning LJ Cutoff in mdp file

[Mark Abraham]

Hi,

What does the .mdp documentation say for rvdw-switch and rvdw?

Mark

On Tue, Mar 13, 2018 at 11:11 AM Tushar Ranjan Moharana <
tusharranjanmohar...@gmail.com> wrote:

> Hi Everyone,
> I want to use LJ interaction cutoff at 12 Å and treat LJ smoothly between
> 10 and 12 Å. Does the following in .mdp file reflect the same?
>
> rvdw-switch  = 0.2
> rvdw = 1
>
> Kindly Reply.
> Thanks a lot.
> --
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
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Re: [gmx-users] Error with CHARMM36 force field

[laurenmr]

Hi Mark,

Thanks for the reply.

I use GROMACS-5.1.4 and I just use standard Linux editors. Please find 
my mdp file attached.


When I check in the file "old_c36_cmap.itp" I do find very long lines (> 
4095 characters). Could this mean that this force field file is not 
compatible with this version of GROMACS?


Thanks,

Lauren


On 13/03/2018 17:07, Mark Abraham wrote:

Hi,

What version of GROMACS is this? Did you edit your file using an unsuitable
editor, such as anything on Windows?

Mark

On Tue, Mar 13, 2018 at 9:20 AM laurenmr  wrote:


Hi Gromacs Users,

I have downloaded the latest version of the CHARMM36M force field. My
aim is to compare a simulation using CHARMM36M and CHARMM36. In the
forcefield.itp there is an 'if' statement allowing the user to switch to
the old CHARMM36 force field by directing to the old cmap itp:

; Allow the user to specify CHARMM36 parameters, instead
; Default behavior is to use CHARMM36m
#ifdef USE_OLD_C36
#include "old_c36_cmap.itp"
#else
#include "cmap.itp"
#endif

However, when I include "define = -DUSE_OLD_C36" in my .mdp file I
receive this error at the grompp command:

Fatal error:
An input file contains a line longer than 4095 characters, while the
buffer passed to fgets2 has size 4095. The line starts with: 'C NH1 CT1
C NH1 1 24'

Could anyone suggest a way around this or should I download an older
version of CHARMM36 (before CHARMM36M)?

Thanks in advance for the help!

Lauren


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; ions.mdp - used as input into grompp to generate ions.tpr
; Parameters describing what to do, when to stop and what to save
define = -DUSE_OLD_C36 ; Don't use cmap corrections
integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 
1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to 
perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and 
long range forces
cutoff-scheme   = Verlet
ns_type = grid  ; Method to determine neighbor list 
(simple, grid)
coulombtype = PME   ; Treatment of long range electrostatic 
interactions
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)
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Re: [gmx-users] rvdw and rcoulomb

[Ahmed Mashaly]

Thanks guys

It is AMBER ff
Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 
for continuation with no effect on the results? And if I do the other restarts 
starting from 1 or it will give different results?

On Mon, 12 Mar, 2018 at 4:37 pm, Szilárd Páll
> wrote:
>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
>>
>> ==
>>
>>
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Re: [gmx-users] Error with CHARMM36 force field

[laurenmr]

Hi Mark,

Thanks for the reply. I will contact the relevant person!

Thanks,

Lauren


On 13/03/2018 17:40, Mark Abraham wrote:

Hi,

Yes, I guess it must be somehow incompatible. Maybe it worked with an older
version of GROMACS that worked differently - the mdp handling has had some
cleaning up over time, and some buggy behaviours may have been
inadvertently depended on. Perhaps this should be brought to the attention
of whoever maintains that file.

Mark

On Tue, Mar 13, 2018 at 10:17 AM laurenmr 
wrote:


Hi Mark,

Thanks for the reply.

I use GROMACS-5.1.4 and I just use standard Linux editors. Please find
my mdp file attached.

When I check in the file "old_c36_cmap.itp" I do find very long lines (>
4095 characters). Could this mean that this force field file is not
compatible with this version of GROMACS?

Thanks,

Lauren


On 13/03/2018 17:07, Mark Abraham wrote:

Hi,

What version of GROMACS is this? Did you edit your file using an

unsuitable

editor, such as anything on Windows?

Mark

On Tue, Mar 13, 2018 at 9:20 AM laurenmr 

wrote:

Hi Gromacs Users,

I have downloaded the latest version of the CHARMM36M force field. My
aim is to compare a simulation using CHARMM36M and CHARMM36. In the
forcefield.itp there is an 'if' statement allowing the user to switch to
the old CHARMM36 force field by directing to the old cmap itp:

; Allow the user to specify CHARMM36 parameters, instead
; Default behavior is to use CHARMM36m
#ifdef USE_OLD_C36
#include "old_c36_cmap.itp"
#else
#include "cmap.itp"
#endif

However, when I include "define = -DUSE_OLD_C36" in my .mdp file I
receive this error at the grompp command:

Fatal error:
An input file contains a line longer than 4095 characters, while the
buffer passed to fgets2 has size 4095. The line starts with: 'C NH1 CT1
C NH1 1 24'

Could anyone suggest a way around this or should I download an older
version of CHARMM36 (before CHARMM36M)?

Thanks in advance for the help!

Lauren


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Re: [gmx-users] Error with CHARMM36 force field

[laurenmr]

Hi Justin,

Thanks for the reply. Will download now.

Thanks,

Lauren


On 13/03/2018 17:50, Justin Lemkul wrote:



On 3/13/18 5:47 AM, laurenmr wrote:

Hi Mark,

Thanks for the reply. I will contact the relevant person!



This was a bug very briefly when the latest tarball went online. I 
fixed it months ago.


Please just download the latest tarball from 
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs.


-Justin


Thanks,

Lauren


On 13/03/2018 17:40, Mark Abraham wrote:

Hi,

Yes, I guess it must be somehow incompatible. Maybe it worked with 
an older
version of GROMACS that worked differently - the mdp handling has 
had some

cleaning up over time, and some buggy behaviours may have been
inadvertently depended on. Perhaps this should be brought to the 
attention

of whoever maintains that file.

Mark

On Tue, Mar 13, 2018 at 10:17 AM laurenmr 
wrote:


Hi Mark,

Thanks for the reply.

I use GROMACS-5.1.4 and I just use standard Linux editors. Please find
my mdp file attached.

When I check in the file "old_c36_cmap.itp" I do find very long 
lines (>

4095 characters). Could this mean that this force field file is not
compatible with this version of GROMACS?

Thanks,

Lauren


On 13/03/2018 17:07, Mark Abraham wrote:

Hi,

What version of GROMACS is this? Did you edit your file using an

unsuitable

editor, such as anything on Windows?

Mark

On Tue, Mar 13, 2018 at 9:20 AM laurenmr 

wrote:

Hi Gromacs Users,

I have downloaded the latest version of the CHARMM36M force 
field. My

aim is to compare a simulation using CHARMM36M and CHARMM36. In the
forcefield.itp there is an 'if' statement allowing the user to 
switch to

the old CHARMM36 force field by directing to the old cmap itp:

; Allow the user to specify CHARMM36 parameters, instead
; Default behavior is to use CHARMM36m
#ifdef USE_OLD_C36
#include "old_c36_cmap.itp"
#else
#include "cmap.itp"
#endif

However, when I include "define = -DUSE_OLD_C36" in my .mdp file I
receive this error at the grompp command:

Fatal error:
An input file contains a line longer than 4095 characters, while the
buffer passed to fgets2 has size 4095. The line starts with: 'C 
NH1 CT1

C NH1 1 24'

Could anyone suggest a way around this or should I download an older
version of CHARMM36 (before CHARMM36M)?

Thanks in advance for the help!

Lauren


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

[Mark Abraham]

Hi,

On Tue, Mar 13, 2018 at 7:31 AM 신동규  wrote:

> 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.
>

Sure, ordering it to do the thing that the automation wanted to do won't
help.

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).


The error message already suggests some solutions. Get a GCC compiler (.e.g
from dev-toolset packages) that is the latest one supported by your CUDA
library.

Mark
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Re: [gmx-users] Error with CHARMM36 force field

[Justin Lemkul]

On 3/13/18 5:47 AM, laurenmr wrote:

Hi Mark,

Thanks for the reply. I will contact the relevant person!



This was a bug very briefly when the latest tarball went online. I fixed 
it months ago.


Please just download the latest tarball from 
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs.


-Justin


Thanks,

Lauren


On 13/03/2018 17:40, Mark Abraham wrote:

Hi,

Yes, I guess it must be somehow incompatible. Maybe it worked with an 
older
version of GROMACS that worked differently - the mdp handling has had 
some

cleaning up over time, and some buggy behaviours may have been
inadvertently depended on. Perhaps this should be brought to the 
attention

of whoever maintains that file.

Mark

On Tue, Mar 13, 2018 at 10:17 AM laurenmr 
wrote:


Hi Mark,

Thanks for the reply.

I use GROMACS-5.1.4 and I just use standard Linux editors. Please find
my mdp file attached.

When I check in the file "old_c36_cmap.itp" I do find very long 
lines (>

4095 characters). Could this mean that this force field file is not
compatible with this version of GROMACS?

Thanks,

Lauren


On 13/03/2018 17:07, Mark Abraham wrote:

Hi,

What version of GROMACS is this? Did you edit your file using an

unsuitable

editor, such as anything on Windows?

Mark

On Tue, Mar 13, 2018 at 9:20 AM laurenmr 

wrote:

Hi Gromacs Users,

I have downloaded the latest version of the CHARMM36M force field. My
aim is to compare a simulation using CHARMM36M and CHARMM36. In the
forcefield.itp there is an 'if' statement allowing the user to 
switch to

the old CHARMM36 force field by directing to the old cmap itp:

; Allow the user to specify CHARMM36 parameters, instead
; Default behavior is to use CHARMM36m
#ifdef USE_OLD_C36
#include "old_c36_cmap.itp"
#else
#include "cmap.itp"
#endif

However, when I include "define = -DUSE_OLD_C36" in my .mdp file I
receive this error at the grompp command:

Fatal error:
An input file contains a line longer than 4095 characters, while the
buffer passed to fgets2 has size 4095. The line starts with: 'C 
NH1 CT1

C NH1 1 24'

Could anyone suggest a way around this or should I download an older
version of CHARMM36 (before CHARMM36M)?

Thanks in advance for the help!

Lauren


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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] GROMACS 5.1.4 and dssp 2.2.1

[Simon Kit Sang Chu]

Hi João,

Thanks for your suggestion. Unfortunately, the error persists. I thought
-ver 2 was the default value.

Regards,
Simon

2018-03-13 15:58 GMT+08:00 João Henriques :

> "Fatal error: Failed to execute command: Try specifying your dssp version
> with the -ver option."
>
> Did you follow the error message suggestion? With DSSP 2.2.1 you need to
> set "-ver 2" on your gmx do_dssp command.
>
> J
>
> On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu <
> simoncks1...@gmail.com>
> wrote:
>
> > Hi everyone.
> >
> > I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1. It returned
> > an error:
> >
> >
> > Fatal error:
> > Failed to execute command: Try specifying your dssp version with the -ver
> > option.
> >
> >
> > I can run mkdssp and it is placed in bin. Is it a compatibility problem
> > here?
> >
> > Thanks in advance.
> >
> > Regards.
> > Simon
> > --
> > Gromacs Users mailing list
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> >
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Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

[Mark Abraham]

Hi,

gmx do_dssp -h

says everything there is to say about how to get this to work. I've no idea
what mkdssp is, but unless it does the same things as dssp, it won't work.

Mark

On Tue, Mar 13, 2018 at 9:56 AM Simon Kit Sang Chu 
wrote:

> Hi João,
>
> Thanks for your suggestion. Unfortunately, the error persists. I thought
> -ver 2 was the default value.
>
> Regards,
> Simon
>
> 2018-03-13 15:58 GMT+08:00 João Henriques :
>
> > "Fatal error: Failed to execute command: Try specifying your dssp version
> > with the -ver option."
> >
> > Did you follow the error message suggestion? With DSSP 2.2.1 you need to
> > set "-ver 2" on your gmx do_dssp command.
> >
> > J
> >
> > On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu <
> > simoncks1...@gmail.com>
> > wrote:
> >
> > > Hi everyone.
> > >
> > > I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1. It
> returned
> > > an error:
> > >
> > >
> > > Fatal error:
> > > Failed to execute command: Try specifying your dssp version with the
> -ver
> > > option.
> > >
> > >
> > > I can run mkdssp and it is placed in bin. Is it a compatibility problem
> > > here?
> > >
> > > Thanks in advance.
> > >
> > > Regards.
> > > Simon
> > > --
> > > 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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> >
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Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

[Simon Kit Sang Chu]

Thank you, Joe. I re-ensure that dssp works in my case. I tried:

dssp prod-protein.pdb -o test.dssp

The result looks fine without error text.

Simon

2018-03-13 17:24 GMT+08:00 Joe Jordan :

> You can find a dssp binary here http://swift.cmbi.ru.nl/gv/dssp/
> It is also in the ubuntu repo.
> You should to get mkdssp and/or dssp to work on their own and if you can't
> then your problem is not with gmx.
>
> On Tue, Mar 13, 2018 at 10:15 AM, Simon Kit Sang Chu <
> simoncks1...@gmail.com
> > wrote:
>
> > Hi everyone,
> >
> > I linked dssp as mkdssp and it still does not work. I try to run dssp in
> > terminal. This is the result.
> >
> > mkdssp 2.2.1 options:
> >   -h [ --help ] Display help message
> >   -i [ --input ] argInput file
> >   -o [ --output ] arg   Output file, use 'stdout' to output to screen
> >   -v [ --verbose ]  Verbose output
> >   --version Print version
> >   -d [ --debug ] argDebug level (for even more verbose output)
> >
> >
> > Examples:
> >
> > To calculate the secondary structure for the file 1crn.pdb and
> > write the result to a file called 1crn.dssp, you type:
> >
> >   dssp -i 1crn.pdb -o 1crn.dssp
> >
> > Hope it behaves normally.
> >
> > Simon
> >
> > 2018-03-13 17:07 GMT+08:00 Mark Abraham :
> >
> > > Hi,
> > >
> > > gmx do_dssp -h
> > >
> > > says everything there is to say about how to get this to work. I've no
> > idea
> > > what mkdssp is, but unless it does the same things as dssp, it won't
> > work.
> > >
> > > Mark
> > >
> > > On Tue, Mar 13, 2018 at 9:56 AM Simon Kit Sang Chu <
> > simoncks1...@gmail.com
> > > >
> > > wrote:
> > >
> > > > Hi João,
> > > >
> > > > Thanks for your suggestion. Unfortunately, the error persists. I
> > thought
> > > > -ver 2 was the default value.
> > > >
> > > > Regards,
> > > > Simon
> > > >
> > > > 2018-03-13 15:58 GMT+08:00 João Henriques <
> > joao.m.a.henriq...@gmail.com>
> > > :
> > > >
> > > > > "Fatal error: Failed to execute command: Try specifying your dssp
> > > version
> > > > > with the -ver option."
> > > > >
> > > > > Did you follow the error message suggestion? With DSSP 2.2.1 you
> need
> > > to
> > > > > set "-ver 2" on your gmx do_dssp command.
> > > > >
> > > > > J
> > > > >
> > > > > On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu <
> > > > > simoncks1...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > Hi everyone.
> > > > > >
> > > > > > I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1. It
> > > > returned
> > > > > > an error:
> > > > > >
> > > > > >
> > > > > > Fatal error:
> > > > > > Failed to execute command: Try specifying your dssp version with
> > the
> > > > -ver
> > > > > > option.
> > > > > >
> > > > > >
> > > > > > I can run mkdssp and it is placed in bin. Is it a compatibility
> > > problem
> > > > > > here?
> > > > > >
> > > > > > Thanks in advance.
> > > > > >
> > > > > > Regards.
> > > > > > Simon
> > > > > > --
> > > > > > 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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> > > > >
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[gmx-users] Mentioning LJ Cutoff in mdp file

[Tushar Ranjan Moharana]

Hi Everyone,
I want to use LJ interaction cutoff at 12 Å and treat LJ smoothly between
10 and 12 Å. Does the following in .mdp file reflect the same?

rvdw-switch  = 0.2
rvdw = 1

Kindly Reply.
Thanks a lot.
-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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Re: [gmx-users] GMX 2018 and 'distance' pull

[Viveca Lindahl]

Hi Alex,

If you think this is a bug introduced in gromacs 2018, perhaps you could
file a bug report on https://redmine.gromacs.org/? Attaching tpr's (or run
setups) both for the 2018 and the 5.04 version together with an md.log
would be helpful.

--
Viveca


On Tue, Mar 13, 2018 at 7:38 AM, Alex  wrote:

> 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
>
> --
> 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] computation/memory modifications

[Justin Lemkul]

On 3/13/18 2:49 AM, Mahmood Naderan wrote:

No idea? Any feedback is appreciated.


You likely missed my reply:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-March/119068.html

-Justin



Regards,
Mahmood

 On Friday, March 9, 2018, 9:47:33 PM GMT+3:30, Mahmood Naderan 
 wrote:
  
  Hi,

I want to do some tests on the lysozyme tutorial. Assume that the tutorial with 
the default parameters which is run for 10ps, takes X seconds wall clock time. 
If I want to increase the wall clock time, I can simply run for 100ps. However, 
that is not what I want.
I want to increase the amount of computation for every step, e.g. 1ps. Therefore I 
want another run for 10ps which takes Y seconds wall clock time where Y>X. I 
also want to increase the memory usage for each step compared to the default 
values in the tutorial.
May I know which parameters are chosen for those purposes?

Regards,
Mahmood


--
==

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] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?

[Douwe Pollmann]

Hi Mark,

I use the Cb's to define a plane, and I use virtual sites to place beads in
that plane.
So the Cb's do not have non-bonded interactions with other beads, but they
feel a force via the virtual sites.
The problem is that my simulations are very unstable and that this is
probably due to the fact LINCS and SHAKE have difficulties with the so
called angle constraints.

Douwe

2018-03-13 9:37 GMT+01:00 Mark Abraham :

> Hi,
>
> If there's no interactions with CB then what's the point?
>
> Mark
>
> On Tue, Mar 13, 2018, 09:28 Douwe Pollmann 
> wrote:
>
> > Hi Mark,
> >
> > Thanks for your reaction!
> >
> > 2018-03-12 18:08 GMT+01:00 Mark Abraham :
> >
> > > Hi,
> > >
> > > On Mon, Mar 12, 2018 at 4:19 PM Douwe Pollmann <
> douwepollm...@gmail.com>
> > > 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.
> > >
> >
> > I will play a bit more with the values for lincs-order and lincs-iter, or
> > the value for shake-tol.
> >
> >
> > > 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.
> > >
> >
> > There is no interaction with the Cb's and the other atoms in the system,
> I
> > excluded them all in the energygrp-excl. So unfortunately that isn't the
> > solution..
> >
> >
> > >
> > > > 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
> > >
> >
> > Yeah okay, true :)
> >
> >
> > > 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.
> > >
> >
> > I also thought of virtual sites and I came to the same conclusion as you,
> > so I was already afraid for this answer..
> > Thanks for thinking along!
> >
> >
> > >
> > > Mark
> > >
> > > Thank you in advance for any help!
> > > >
> > > > Kind regards,
> > > > Douwe Pollmann
> > > > --
> > > > 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 

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

[Mark Abraham]

Hi,

If there's no interactions with CB then what's the point?

Mark

On Tue, Mar 13, 2018, 09:28 Douwe Pollmann  wrote:

> Hi Mark,
>
> Thanks for your reaction!
>
> 2018-03-12 18:08 GMT+01:00 Mark Abraham :
>
> > 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.
> >
>
> I will play a bit more with the values for lincs-order and lincs-iter, or
> the value for shake-tol.
>
>
> > 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.
> >
>
> There is no interaction with the Cb's and the other atoms in the system, I
> excluded them all in the energygrp-excl. So unfortunately that isn't the
> solution..
>
>
> >
> > > 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
> >
>
> Yeah okay, true :)
>
>
> > 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.
> >
>
> I also thought of virtual sites and I came to the same conclusion as you,
> so I was already afraid for this answer..
> Thanks for thinking along!
>
>
> >
> > Mark
> >
> > Thank you in advance for any help!
> > >
> > > Kind regards,
> > > Douwe Pollmann
> > > --
> > > 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!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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>
> * Please search the archive at
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> posting!
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Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

[Mateusz Bieniek]

I had a similar issue with dssp which suddenly stopped working. Switching
to x86 binary worked for me.

Linux Arch

Mat

On Tue, 13 Mar 2018, 09:25 Joe Jordan,  wrote:

> You can find a dssp binary here http://swift.cmbi.ru.nl/gv/dssp/
> It is also in the ubuntu repo.
> You should to get mkdssp and/or dssp to work on their own and if you can't
> then your problem is not with gmx.
>
> On Tue, Mar 13, 2018 at 10:15 AM, Simon Kit Sang Chu <
> simoncks1...@gmail.com
> > wrote:
>
> > Hi everyone,
> >
> > I linked dssp as mkdssp and it still does not work. I try to run dssp in
> > terminal. This is the result.
> >
> > mkdssp 2.2.1 options:
> >   -h [ --help ] Display help message
> >   -i [ --input ] argInput file
> >   -o [ --output ] arg   Output file, use 'stdout' to output to screen
> >   -v [ --verbose ]  Verbose output
> >   --version Print version
> >   -d [ --debug ] argDebug level (for even more verbose output)
> >
> >
> > Examples:
> >
> > To calculate the secondary structure for the file 1crn.pdb and
> > write the result to a file called 1crn.dssp, you type:
> >
> >   dssp -i 1crn.pdb -o 1crn.dssp
> >
> > Hope it behaves normally.
> >
> > Simon
> >
> > 2018-03-13 17:07 GMT+08:00 Mark Abraham :
> >
> > > Hi,
> > >
> > > gmx do_dssp -h
> > >
> > > says everything there is to say about how to get this to work. I've no
> > idea
> > > what mkdssp is, but unless it does the same things as dssp, it won't
> > work.
> > >
> > > Mark
> > >
> > > On Tue, Mar 13, 2018 at 9:56 AM Simon Kit Sang Chu <
> > simoncks1...@gmail.com
> > > >
> > > wrote:
> > >
> > > > Hi João,
> > > >
> > > > Thanks for your suggestion. Unfortunately, the error persists. I
> > thought
> > > > -ver 2 was the default value.
> > > >
> > > > Regards,
> > > > Simon
> > > >
> > > > 2018-03-13 15:58 GMT+08:00 João Henriques <
> > joao.m.a.henriq...@gmail.com>
> > > :
> > > >
> > > > > "Fatal error: Failed to execute command: Try specifying your dssp
> > > version
> > > > > with the -ver option."
> > > > >
> > > > > Did you follow the error message suggestion? With DSSP 2.2.1 you
> need
> > > to
> > > > > set "-ver 2" on your gmx do_dssp command.
> > > > >
> > > > > J
> > > > >
> > > > > On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu <
> > > > > simoncks1...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > Hi everyone.
> > > > > >
> > > > > > I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1. It
> > > > returned
> > > > > > an error:
> > > > > >
> > > > > >
> > > > > > Fatal error:
> > > > > > Failed to execute command: Try specifying your dssp version with
> > the
> > > > -ver
> > > > > > option.
> > > > > >
> > > > > >
> > > > > > I can run mkdssp and it is placed in bin. Is it a compatibility
> > > problem
> > > > > > here?
> > > > > >
> > > > > > Thanks in advance.
> > > > > >
> > > > > > Regards.
> > > > > > Simon
> > > > > > --
> > > > > > 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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> > > >
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> > > > posting!
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> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > --
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> > >
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> > > 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.
> > >
> > --
> > 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 

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

[João Henriques]

Ok, there's quite a lot going on here. The mkdssp the OP talks about is the
default name for the executable you get upon compilation from source.
Naming it dssp makes more sense, so that's why I suggested making a link
called dssp. Either way, it shouldn't matter because if you give the right
path to mkdssp or dssp or whatever name you give it, it should work.

If the standalone execution of dssp works, the problem must be with the
export.

Please confirm that you have exported the DSSP environment variable
correctly. Type "$DSSP -h" for example. If that works, then there's no
reason for gmx do_dssp to not work.

P.S.: dssp is notoriously tricky to compile, e.g. the static flag issue. I
also recently noticed that with boost >= 1.65.1, the code gets seriously
broken and needs some major modifications (see https://pastebin.com/NiQJkjuC
).

J





On Tue, Mar 13, 2018 at 10:30 AM, Simon Kit Sang Chu  wrote:

> Thank you, Joe. I re-ensure that dssp works in my case. I tried:
>
> dssp prod-protein.pdb -o test.dssp
>
> The result looks fine without error text.
>
> Simon
>
> 2018-03-13 17:24 GMT+08:00 Joe Jordan :
>
> > You can find a dssp binary here http://swift.cmbi.ru.nl/gv/dssp/
> > It is also in the ubuntu repo.
> > You should to get mkdssp and/or dssp to work on their own and if you
> can't
> > then your problem is not with gmx.
> >
> > On Tue, Mar 13, 2018 at 10:15 AM, Simon Kit Sang Chu <
> > simoncks1...@gmail.com
> > > wrote:
> >
> > > Hi everyone,
> > >
> > > I linked dssp as mkdssp and it still does not work. I try to run dssp
> in
> > > terminal. This is the result.
> > >
> > > mkdssp 2.2.1 options:
> > >   -h [ --help ] Display help message
> > >   -i [ --input ] argInput file
> > >   -o [ --output ] arg   Output file, use 'stdout' to output to screen
> > >   -v [ --verbose ]  Verbose output
> > >   --version Print version
> > >   -d [ --debug ] argDebug level (for even more verbose output)
> > >
> > >
> > > Examples:
> > >
> > > To calculate the secondary structure for the file 1crn.pdb and
> > > write the result to a file called 1crn.dssp, you type:
> > >
> > >   dssp -i 1crn.pdb -o 1crn.dssp
> > >
> > > Hope it behaves normally.
> > >
> > > Simon
> > >
> > > 2018-03-13 17:07 GMT+08:00 Mark Abraham :
> > >
> > > > Hi,
> > > >
> > > > gmx do_dssp -h
> > > >
> > > > says everything there is to say about how to get this to work. I've
> no
> > > idea
> > > > what mkdssp is, but unless it does the same things as dssp, it won't
> > > work.
> > > >
> > > > Mark
> > > >
> > > > On Tue, Mar 13, 2018 at 9:56 AM Simon Kit Sang Chu <
> > > simoncks1...@gmail.com
> > > > >
> > > > wrote:
> > > >
> > > > > Hi João,
> > > > >
> > > > > Thanks for your suggestion. Unfortunately, the error persists. I
> > > thought
> > > > > -ver 2 was the default value.
> > > > >
> > > > > Regards,
> > > > > Simon
> > > > >
> > > > > 2018-03-13 15:58 GMT+08:00 João Henriques <
> > > joao.m.a.henriq...@gmail.com>
> > > > :
> > > > >
> > > > > > "Fatal error: Failed to execute command: Try specifying your dssp
> > > > version
> > > > > > with the -ver option."
> > > > > >
> > > > > > Did you follow the error message suggestion? With DSSP 2.2.1 you
> > need
> > > > to
> > > > > > set "-ver 2" on your gmx do_dssp command.
> > > > > >
> > > > > > J
> > > > > >
> > > > > > On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu <
> > > > > > simoncks1...@gmail.com>
> > > > > > wrote:
> > > > > >
> > > > > > > Hi everyone.
> > > > > > >
> > > > > > > I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1.
> It
> > > > > returned
> > > > > > > an error:
> > > > > > >
> > > > > > >
> > > > > > > Fatal error:
> > > > > > > Failed to execute command: Try specifying your dssp version
> with
> > > the
> > > > > -ver
> > > > > > > option.
> > > > > > >
> > > > > > >
> > > > > > > I can run mkdssp and it is placed in bin. Is it a compatibility
> > > > problem
> > > > > > > here?
> > > > > > >
> > > > > > > Thanks in advance.
> > > > > > >
> > > > > > > Regards.
> > > > > > > Simon
> > > > > > > --
> > > > > > > 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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> Support/Mailing_Lists
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> > > > or
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Re: [gmx-users] rvdw and rcoulomb

[Justin Lemkul]

On 3/13/18 5:17 AM, Ahmed Mashaly wrote:

Thanks guys

It is AMBER ff
Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 
for continuation with no effect on the results? And if I do the other restarts 
starting from 1 or it will give different results?


You shouldn't switch physical models mid-simulation. Start over using 
the correct value (1.2 nm is incorrect for AMBER, anyway).


-Justin


On Mon, 12 Mar, 2018 at 4:37 pm, Szilárd Páll

 wrote:
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

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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303 Engel Hall
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Re: [gmx-users] Error with CHARMM36 force field

[Mark Abraham]

Hi,

Yes, I guess it must be somehow incompatible. Maybe it worked with an older
version of GROMACS that worked differently - the mdp handling has had some
cleaning up over time, and some buggy behaviours may have been
inadvertently depended on. Perhaps this should be brought to the attention
of whoever maintains that file.

Mark

On Tue, Mar 13, 2018 at 10:17 AM laurenmr 
wrote:

> Hi Mark,
>
> Thanks for the reply.
>
> I use GROMACS-5.1.4 and I just use standard Linux editors. Please find
> my mdp file attached.
>
> When I check in the file "old_c36_cmap.itp" I do find very long lines (>
> 4095 characters). Could this mean that this force field file is not
> compatible with this version of GROMACS?
>
> Thanks,
>
> Lauren
>
>
> On 13/03/2018 17:07, Mark Abraham wrote:
> > Hi,
> >
> > What version of GROMACS is this? Did you edit your file using an
> unsuitable
> > editor, such as anything on Windows?
> >
> > Mark
> >
> > On Tue, Mar 13, 2018 at 9:20 AM laurenmr 
> wrote:
> >
> >> Hi Gromacs Users,
> >>
> >> I have downloaded the latest version of the CHARMM36M force field. My
> >> aim is to compare a simulation using CHARMM36M and CHARMM36. In the
> >> forcefield.itp there is an 'if' statement allowing the user to switch to
> >> the old CHARMM36 force field by directing to the old cmap itp:
> >>
> >> ; Allow the user to specify CHARMM36 parameters, instead
> >> ; Default behavior is to use CHARMM36m
> >> #ifdef USE_OLD_C36
> >> #include "old_c36_cmap.itp"
> >> #else
> >> #include "cmap.itp"
> >> #endif
> >>
> >> However, when I include "define = -DUSE_OLD_C36" in my .mdp file I
> >> receive this error at the grompp command:
> >>
> >> Fatal error:
> >> An input file contains a line longer than 4095 characters, while the
> >> buffer passed to fgets2 has size 4095. The line starts with: 'C NH1 CT1
> >> C NH1 1 24'
> >>
> >> Could anyone suggest a way around this or should I download an older
> >> version of CHARMM36 (before CHARMM36M)?
> >>
> >> Thanks in advance for the help!
> >>
> >> Lauren
> >>
> >>
> >> --
> >> 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] GMX 2018 and 'distance' pull

[Justin Lemkul]

On 3/13/18 2:38 AM, Alex wrote:

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?




You may have a situation that requires manual assignment of 
pull_group1_pbcatom1, as the automatic choice of "choose a number in the 
middle of the list" may be inappropriate in your case. It works well for 
a globular protein, but for a sheet of material, probably you're getting 
an incorrect check from mdrun.


The pull code was basically re-written in version 5.1, hence why you may 
not have seen an issue back in 5.0.4.


-Justin

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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Re: [gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?

[Douwe Pollmann]

Hi Mark,

Thanks for your reaction!

2018-03-12 18:08 GMT+01:00 Mark Abraham :

> 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.
>

I will play a bit more with the values for lincs-order and lincs-iter, or
the value for shake-tol.


> 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.
>

There is no interaction with the Cb's and the other atoms in the system, I
excluded them all in the energygrp-excl. So unfortunately that isn't the
solution..


>
> > 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
>

Yeah okay, true :)


> 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.
>

I also thought of virtual sites and I came to the same conclusion as you,
so I was already afraid for this answer..
Thanks for thinking along!


>
> Mark
>
> Thank you in advance for any help!
> >
> > Kind regards,
> > Douwe Pollmann
> > --
> > Gromacs Users mailing list
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Re: [gmx-users] Error with CHARMM36 force field

[Mark Abraham]

Hi,

What version of GROMACS is this? Did you edit your file using an unsuitable
editor, such as anything on Windows?

Mark

On Tue, Mar 13, 2018 at 9:20 AM laurenmr  wrote:

> Hi Gromacs Users,
>
> I have downloaded the latest version of the CHARMM36M force field. My
> aim is to compare a simulation using CHARMM36M and CHARMM36. In the
> forcefield.itp there is an 'if' statement allowing the user to switch to
> the old CHARMM36 force field by directing to the old cmap itp:
>
> ; Allow the user to specify CHARMM36 parameters, instead
> ; Default behavior is to use CHARMM36m
> #ifdef USE_OLD_C36
> #include "old_c36_cmap.itp"
> #else
> #include "cmap.itp"
> #endif
>
> However, when I include "define = -DUSE_OLD_C36" in my .mdp file I
> receive this error at the grompp command:
>
> Fatal error:
> An input file contains a line longer than 4095 characters, while the
> buffer passed to fgets2 has size 4095. The line starts with: 'C NH1 CT1
> C NH1 1 24'
>
> Could anyone suggest a way around this or should I download an older
> version of CHARMM36 (before CHARMM36M)?
>
> Thanks in advance for the help!
>
> Lauren
>
>
> --
> Gromacs Users mailing list
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Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

[João Henriques]

Is the export consistent with the executable name?

J

On Tue, Mar 13, 2018 at 9:55 AM, Simon Kit Sang Chu 
wrote:

> Hi João,
>
> Thanks for your suggestion. Unfortunately, the error persists. I thought
> -ver 2 was the default value.
>
> Regards,
> Simon
>
> 2018-03-13 15:58 GMT+08:00 João Henriques :
>
> > "Fatal error: Failed to execute command: Try specifying your dssp version
> > with the -ver option."
> >
> > Did you follow the error message suggestion? With DSSP 2.2.1 you need to
> > set "-ver 2" on your gmx do_dssp command.
> >
> > J
> >
> > On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu <
> > simoncks1...@gmail.com>
> > wrote:
> >
> > > Hi everyone.
> > >
> > > I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1. It
> returned
> > > an error:
> > >
> > >
> > > Fatal error:
> > > Failed to execute command: Try specifying your dssp version with the
> -ver
> > > option.
> > >
> > >
> > > I can run mkdssp and it is placed in bin. Is it a compatibility problem
> > > here?
> > >
> > > Thanks in advance.
> > >
> > > Regards.
> > > Simon
> > > --
> > > Gromacs Users mailing list
> > >
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Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

[Joe Jordan]

You can find a dssp binary here http://swift.cmbi.ru.nl/gv/dssp/
It is also in the ubuntu repo.
You should to get mkdssp and/or dssp to work on their own and if you can't
then your problem is not with gmx.

On Tue, Mar 13, 2018 at 10:15 AM, Simon Kit Sang Chu  wrote:

> Hi everyone,
>
> I linked dssp as mkdssp and it still does not work. I try to run dssp in
> terminal. This is the result.
>
> mkdssp 2.2.1 options:
>   -h [ --help ] Display help message
>   -i [ --input ] argInput file
>   -o [ --output ] arg   Output file, use 'stdout' to output to screen
>   -v [ --verbose ]  Verbose output
>   --version Print version
>   -d [ --debug ] argDebug level (for even more verbose output)
>
>
> Examples:
>
> To calculate the secondary structure for the file 1crn.pdb and
> write the result to a file called 1crn.dssp, you type:
>
>   dssp -i 1crn.pdb -o 1crn.dssp
>
> Hope it behaves normally.
>
> Simon
>
> 2018-03-13 17:07 GMT+08:00 Mark Abraham :
>
> > Hi,
> >
> > gmx do_dssp -h
> >
> > says everything there is to say about how to get this to work. I've no
> idea
> > what mkdssp is, but unless it does the same things as dssp, it won't
> work.
> >
> > Mark
> >
> > On Tue, Mar 13, 2018 at 9:56 AM Simon Kit Sang Chu <
> simoncks1...@gmail.com
> > >
> > wrote:
> >
> > > Hi João,
> > >
> > > Thanks for your suggestion. Unfortunately, the error persists. I
> thought
> > > -ver 2 was the default value.
> > >
> > > Regards,
> > > Simon
> > >
> > > 2018-03-13 15:58 GMT+08:00 João Henriques <
> joao.m.a.henriq...@gmail.com>
> > :
> > >
> > > > "Fatal error: Failed to execute command: Try specifying your dssp
> > version
> > > > with the -ver option."
> > > >
> > > > Did you follow the error message suggestion? With DSSP 2.2.1 you need
> > to
> > > > set "-ver 2" on your gmx do_dssp command.
> > > >
> > > > J
> > > >
> > > > On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu <
> > > > simoncks1...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi everyone.
> > > > >
> > > > > I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1. It
> > > returned
> > > > > an error:
> > > > >
> > > > >
> > > > > Fatal error:
> > > > > Failed to execute command: Try specifying your dssp version with
> the
> > > -ver
> > > > > option.
> > > > >
> > > > >
> > > > > I can run mkdssp and it is placed in bin. Is it a compatibility
> > problem
> > > > > here?
> > > > >
> > > > > Thanks in advance.
> > > > >
> > > > > Regards.
> > > > > Simon
> > > > > --
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> > > > >
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[gmx-users] Regarding calculation of Hydrogen-Bond

[Dilip H N]

Hello,
I want to calculate Hydrogen bonding between C-alpha of glycine and the
oxygen atom of water molecules.
So, i gave the command as:-

gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg

but i got the error as:
Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
Found 0 donors and 511 acceptors
No Donors found
---
Program: gmx hbond, version 2016.2
Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
Fatal error:
Nothing to be done

So, how can i solve this issue..?? Is there no any Hydrogen bonding between
this..?? (I think there is some hydrogen bonding present ...)

Any suggestions are appreciated.

Thank you.

-- 
With Best Regards,

DILIP.H.N
PhD Student



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Re: [gmx-users] Regarding calculation of Hydrogen-Bond

[Erik Marklund]

Dear Dilip,

The Calpha is not considered a hbond donor.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 13 Mar 2018, at 11:03, Dilip H N 
> wrote:

Hello,
I want to calculate Hydrogen bonding between C-alpha of glycine and the
oxygen atom of water molecules.
So, i gave the command as:-

gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg

but i got the error as:
Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
Found 0 donors and 511 acceptors
No Donors found
---
Program: gmx hbond, version 2016.2
Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
Fatal error:
Nothing to be done

So, how can i solve this issue..?? Is there no any Hydrogen bonding between
this..?? (I think there is some hydrogen bonding present ...)

Any suggestions are appreciated.

Thank you.

--
With Best Regards,

DILIP.H.N
PhD Student



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Re: [gmx-users] GMX 2018 and 'distance' pull

[Justin Lemkul]

On 3/13/18 7:16 AM, Justin Lemkul wrote:



On 3/13/18 2:38 AM, Alex wrote:

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?




You may have a situation that requires manual assignment of 
pull_group1_pbcatom1, as the automatic choice of 


Sorry, that should be pull_group1_pbcatom. Must remind myself not to 
email before coffee...


-Justin

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Virginia Tech Department of Biochemistry

303 Engel Hall
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Re: [gmx-users] rvdw and rcoulomb

[Ahmed Mashaly]

Dear Justin,

What do you mean by incorrect?
I understand it is higher than it should be (0.8 - 1 nm), it will consume more 
time, but won't give wrong results, am I correct? 
Kind Regards,
Ahmed 


From: Justin Lemkul 
To: gmx-us...@gromacs.org 
Sent: Tuesday, March 13, 2018 12:18 PM
Subject: Re: [gmx-users] rvdw and rcoulomb





On 3/13/18 5:17 AM, Ahmed Mashaly wrote:
> Thanks guys
>
> It is AMBER ff
> Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 
> for continuation with no effect on the results? And if I do the other 
> restarts starting from 1 or it will give different results?

You shouldn't switch physical models mid-simulation. Start over using 
the correct value (1.2 nm is incorrect for AMBER, anyway).

-Justin

> On Mon, 12 Mar, 2018 at 4:37 pm, Szilárd Páll
>>  wrote:
>> 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
>>>
>>> ==
>>>
>>>
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==

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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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Re: [gmx-users] rvdw and rcoulomb

[Justin Lemkul]

On 3/13/18 7:23 AM, Ahmed Mashaly wrote:

Dear Justin,

What do you mean by incorrect?
I understand it is higher than it should be (0.8 - 1 nm), it will consume more 
time, but won't give wrong results, am I correct?


With PME, the value of rcoulomb becomes somewhat irrelevant, but in 
general, one should *not* deviate from prescribed force field cutoff 
values. Force fields are parametrized under a certain set of 
assumptions. If you then deviate from those assumptions, you potentially 
imbalance forces. The simulation will happily run and potentially 
produce incorrect results.


Find the proper values in primary literature (something everyone should 
do before even deciding on a force field) and use those values. GROMACS 
will tune rcoulomb slightly for PME performance reasons, and this is 
fine, but don't go messing with the stock values haphazardly.


-Justin


Kind Regards,
Ahmed


From: Justin Lemkul 
To: gmx-us...@gromacs.org
Sent: Tuesday, March 13, 2018 12:18 PM
Subject: Re: [gmx-users] rvdw and rcoulomb





On 3/13/18 5:17 AM, Ahmed Mashaly wrote:

Thanks guys

It is AMBER ff
Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 
for continuation with no effect on the results? And if I do the other restarts 
starting from 1 or it will give different results?

You shouldn't switch physical models mid-simulation. Start over using
the correct value (1.2 nm is incorrect for AMBER, anyway).

-Justin


On Mon, 12 Mar, 2018 at 4:37 pm, Szilárd Páll

 wrote:
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

--
==

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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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Assistant Professor
Virginia Tech Department of Biochemistry

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340 West Campus Dr.
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Re: [gmx-users] Regarding calculation of Hydrogen-Bond

[Jeremy T First]

Hi Dilip,

There is quite a bit of literature, especially recently, that considers the
alpha carbon as a hydrogen bond donor. How well this is represented in your
simulation will depend on your force field.

You will likely need to develop your own gromacs tool to calculate this,
but it should be quite easy. We recently wrote a tool that does something
very similar, but you would need to edit it for your own purposes. If you
are interested in using our code as a template, feel free to contact me off
list.

Good luck!
Jeremy




Jeremy Todd First
Webb Research Group
University of Texas at Austin
jeremy_fi...@utexas.edu
(443) 243-1187

On Tue, Mar 13, 2018 at 7:25 AM, Erik Marklund 
wrote:

> The point is that Calpha don’t form hydrogen bonds.
>
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se
>
> On 13 Mar 2018, at 13:20, Dilip H N > wrote:
>
> Then how can i calculate the hydrogen bonding between C-alpha and Oxygen
> atom of water molecules..??
> What are the other possible ways..??
>
>
>
>  Sent with Mailtrack
>  signaturevirality& gmail_medium=signature_campaign=signaturevirality&>>
>
> On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund  mailto:erik.markl...@kemi.uu.se>>
> wrote:
>
> Dear Dilip,
>
> The Calpha is not considered a hbond donor.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se erik.markl...@kemi.uu.se>
>
> On 13 Mar 2018, at 11:03, Dilip H N  cy16f01.di...@nitk.edu.in>> wrote:
>
> Hello,
> I want to calculate Hydrogen bonding between C-alpha of glycine and the
> oxygen atom of water molecules.
> So, i gave the command as:-
>
> gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg
>
> but i got the error as:
> Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
> Found 0 donors and 511 acceptors
> No Donors found
> ---
> Program: gmx hbond, version 2016.2
> Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
> Fatal error:
> Nothing to be done
>
> So, how can i solve this issue..?? Is there no any Hydrogen bonding between
> this..?? (I think there is some hydrogen bonding present ...)
>
> Any suggestions are appreciated.
>
> Thank you.
>
> --
> With Best Regards,
>
> DILIP.H.N
> PhD Student
>
>
>
> ‌
>  Sent with Mailtrack
>  signaturevirality&>
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>
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
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Re: [gmx-users] computation/memory modifications

[Justin Lemkul]

On 3/13/18 9:50 AM, Mahmood Naderan wrote:

Sorry about that. I didn't see that in the inbox. Excuse me...
What am I thinking about are some notes in the tutorial. For example



The above command centers the protein in the box (-c), and places it at least 1.0 
nm from the box >edge (-d 1.0). The box type is defined as a cube (-bt cubic)

So, can I make a bigger problem by setting that to 4.0 nm? What about other box 
types?


A cubic box is the least efficient, so to achieve your goal of a slower 
simulation, stick with a cube. Increasing the buffer size around the 
protein will lead to more waters being added.





[ molecules ]
; Compound  #mols
Protein_A 1
SOL   10824
CL    8

I see 8 green points in the figure in that page. Can I increase that to put 
more molecules in the cube?
What are the blue dots in the figure? Are they atoms? If I want to increase the 
number of atoms, should I use another pdb file and run pdb2gmx again?


The 8 Cl- ions balance the charge on the protein. Don't try to change this.

The blue atoms you see are water.




; Name   nrexcl
Protein_A    3

Can I blindly increase that 3?


No, because then you're going to start breaking the model physics, 
whether or not you care I don't know.



Can I use another pdb file (other than 1AKI) and follow the same procedure?


Generally, yes, but don't follow it exactly because the number of ions 
added depends on the charge on the protein.


-Justin


Generally, the type of my questions are like those.




Regards,
Mahmood







On Tuesday, March 13, 2018, 2:48:35 PM GMT+3:30, Justin Lemkul 
 wrote:





On 3/13/18 2:49 AM, Mahmood Naderan wrote:

No idea? Any feedback is appreciated.

You likely missed my reply:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-March/119068.html

-Justin




--
==

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

303 Engel Hall
340 West Campus Dr.
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jalem...@vt.edu | (540) 231-3129
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Re: [gmx-users] Regarding calculation of Hydrogen-Bond

[Erik Marklund]

The point is that Calpha don’t form hydrogen bonds.

Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 13 Mar 2018, at 13:20, Dilip H N 
> wrote:

Then how can i calculate the hydrogen bonding between C-alpha and Oxygen
atom of water molecules..??
What are the other possible ways..??



 Sent with Mailtrack
>

On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund 
>
wrote:

Dear Dilip,

The Calpha is not considered a hbond donor.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 13 Mar 2018, at 11:03, Dilip H N 
mailto:cy16f01.di...@nitk.edu.in>>> wrote:

Hello,
I want to calculate Hydrogen bonding between C-alpha of glycine and the
oxygen atom of water molecules.
So, i gave the command as:-

gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg

but i got the error as:
Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
Found 0 donors and 511 acceptors
No Donors found
---
Program: gmx hbond, version 2016.2
Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
Fatal error:
Nothing to be done

So, how can i solve this issue..?? Is there no any Hydrogen bonding between
this..?? (I think there is some hydrogen bonding present ...)

Any suggestions are appreciated.

Thank you.

--
With Best Regards,

DILIP.H.N
PhD Student



‌
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Re: [gmx-users] GMX 2018 and 'distance' pull

[Justin Lemkul]

On 3/13/18 10:17 AM, Alex wrote:

Justin,
You may have a situation that requires manual assignment of 
pull_group1_pbcatom1, as the automatic choice of 


Sorry, that should be pull_group1_pbcatom. Must remind myself not to 
email before coffee...



Did you mean pull_group2_pbcatom? In my case:

pull_group1_name    = K
pull_group2_name    = CNT

The language for 5.1 pull is (you be the judge on how clear it is):

pull-group1-pbcatom 



   (0) The reference atom for the treatment of periodic boundary
   conditions inside the group (this has no effect on the treatment of
   the pbc between groups). This option is only important when the
   diameter of the pull group is larger than half the shortest box
   vector. For determining the COM, all atoms in the group are put at
   their periodic image which is closest topull-group1-pbcatom
.
   A value of 0 means that the middle atom (number wise) is used. This
   parameter is not used withpull-group1-geometrycylinder. A value of
   -1 turns on cosine weighting, which is useful for a group of
   molecules in a periodic system,/e.g./a water slab (see Engin et al.
   J. Chem. Phys. B 2010).

Indeed, my group2 is a membrane that is wider than the shortest 
half-box. I am assuming it would be a single atom belonging to the 
pore region...




Yes, pull_group2_pbcatom, not 1.

-Justin


Thanks,

Alex


--
==

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

303 Engel Hall
340 West Campus Dr.
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Re: [gmx-users] Regarding calculation of Hydrogen-Bond

[Dilip H N]

Then how can i calculate the hydrogen bonding between C-alpha and Oxygen
atom of water molecules..??
What are the other possible ways..??



 Sent with Mailtrack


On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund 
wrote:

> Dear Dilip,
>
> The Calpha is not considered a hbond donor.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se
>
> On 13 Mar 2018, at 11:03, Dilip H N > wrote:
>
> Hello,
> I want to calculate Hydrogen bonding between C-alpha of glycine and the
> oxygen atom of water molecules.
> So, i gave the command as:-
>
> gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg
>
> but i got the error as:
> Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
> Found 0 donors and 511 acceptors
> No Donors found
> ---
> Program: gmx hbond, version 2016.2
> Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
> Fatal error:
> Nothing to be done
>
> So, how can i solve this issue..?? Is there no any Hydrogen bonding between
> this..?? (I think there is some hydrogen bonding present ...)
>
> Any suggestions are appreciated.
>
> Thank you.
>
> --
> With Best Regards,
>
> DILIP.H.N
> PhD Student
>
>
>
> ‌
>  Sent with Mailtrack
>  signaturevirality&>
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] Error while Installing GROMACS 2018 on Dell EMC T640(Xeon Gold 6152) with Tesla K880 GPU (RHEL 7.3)

[신동규]

Dear Mark,

Thank you for your kind suggestion.
I also read your other suggestion but I did not know what your solution
meant at that time.

I installed devtoolset-6 (7 is not working) in RHEL and commanded cmake
successfully.

Thank you again

Dongkyu



2018-03-13 18:04 GMT+09:00 Mark Abraham :

> Hi,
>
> On Tue, Mar 13, 2018 at 7:31 AM 신동규  wrote:
>
> > 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.
> >
>
> Sure, ordering it to do the thing that the automation wanted to do won't
> help.
>
> 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).
>
>
> The error message already suggests some solutions. Get a GCC compiler (.e.g
> from dev-toolset packages) that is the latest one supported by your CUDA
> library.
>
> Mark
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Re: [gmx-users] Regarding calculation of Hydrogen-Bond

[Erik Marklund]

A shortcut would be to only look at the C-O distance, which can be done with 
gmx hbond without modification.

Kind regards,
Erik

> On 13 Mar 2018, at 15:01, Jeremy T First  wrote:
> 
> Hi Dilip,
> 
> There is quite a bit of literature, especially recently, that considers the
> alpha carbon as a hydrogen bond donor. How well this is represented in your
> simulation will depend on your force field.
> 
> You will likely need to develop your own gromacs tool to calculate this,
> but it should be quite easy. We recently wrote a tool that does something
> very similar, but you would need to edit it for your own purposes. If you
> are interested in using our code as a template, feel free to contact me off
> list.
> 
> Good luck!
> Jeremy
> 
> 
> 
> 
> Jeremy Todd First
> Webb Research Group
> University of Texas at Austin
> jeremy_fi...@utexas.edu
> (443) 243-1187
> 
> On Tue, Mar 13, 2018 at 7:25 AM, Erik Marklund 
> wrote:
> 
>> The point is that Calpha don’t form hydrogen bonds.
>> 
>> Erik
>> __
>> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
>> Department of Chemistry – BMC, Uppsala University
>> +46 (0)18 471 4539
>> erik.markl...@kemi.uu.se
>> 
>> On 13 Mar 2018, at 13:20, Dilip H N  cy16f01.di...@nitk.edu.in>> wrote:
>> 
>> Then how can i calculate the hydrogen bonding between C-alpha and Oxygen
>> atom of water molecules..??
>> What are the other possible ways..??
>> 
>> 
>> 
>>  Sent with Mailtrack
>> > signaturevirality&> gmail_medium=signature_campaign=signaturevirality&>>
>> 
>> On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund > mailto:erik.markl...@kemi.uu.se>>
>> wrote:
>> 
>> Dear Dilip,
>> 
>> The Calpha is not considered a hbond donor.
>> 
>> Kind regards,
>> Erik
>> __
>> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
>> Department of Chemistry – BMC, Uppsala University
>> +46 (0)18 471 4539
>> erik.markl...@kemi.uu.se> erik.markl...@kemi.uu.se>
>> 
>> On 13 Mar 2018, at 11:03, Dilip H N  cy16f01.di...@nitk.edu.in>> cy16f01.di...@nitk.edu.in>> wrote:
>> 
>> Hello,
>> I want to calculate Hydrogen bonding between C-alpha of glycine and the
>> oxygen atom of water molecules.
>> So, i gave the command as:-
>> 
>> gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg
>> 
>> but i got the error as:
>> Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
>> Found 0 donors and 511 acceptors
>> No Donors found
>> ---
>> Program: gmx hbond, version 2016.2
>> Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
>> Fatal error:
>> Nothing to be done
>> 
>> So, how can i solve this issue..?? Is there no any Hydrogen bonding between
>> this..?? (I think there is some hydrogen bonding present ...)
>> 
>> Any suggestions are appreciated.
>> 
>> Thank you.
>> 
>> --
>> With Best Regards,
>> 
>> DILIP.H.N
>> PhD Student
>> 
>> 
>> 
>> ‌
>>  Sent with Mailtrack
>> > signaturevirality&>
>> --
>> 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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>> 
>> * 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.org>> 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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>> 
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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> gromacs.org>.
>> 
>> 
>> 
>> 
>> --
>> With Best Regards,
>> 
>> DILIP.H.N
>> Ph.D Student
>> --
>> 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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>> send a mail to gmx-users-requ...@gromacs.org> gromacs.org>.
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Re: [gmx-users] computation/memory modifications

[Mahmood Naderan]

Sorry about that. I didn't see that in the inbox. Excuse me...
What am I thinking about are some notes in the tutorial. For example


>The above command centers the protein in the box (-c), and places it at least 
>1.0 nm from the box >edge (-d 1.0). The box type is defined as a cube (-bt 
>cubic)

So, can I make a bigger problem by setting that to 4.0 nm? What about other box 
types?


>[ molecules ]
>; Compound  #mols
>Protein_A 1
>SOL   10824
>CL    8

I see 8 green points in the figure in that page. Can I increase that to put 
more molecules in the cube?
What are the blue dots in the figure? Are they atoms? If I want to increase the 
number of atoms, should I use another pdb file and run pdb2gmx again?


>; Name   nrexcl
>Protein_A    3

Can I blindly increase that 3?

Can I use another pdb file (other than 1AKI) and follow the same procedure? 

Generally, the type of my questions are like those.




Regards,
Mahmood







On Tuesday, March 13, 2018, 2:48:35 PM GMT+3:30, Justin Lemkul 
 wrote: 





On 3/13/18 2:49 AM, Mahmood Naderan wrote:
> No idea? Any feedback is appreciated.

You likely missed my reply:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-March/119068.html

-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] GMX 2018 and 'distance' pull

[Alex]

Justin,
You may have a situation that requires manual assignment of 
pull_group1_pbcatom1, as the automatic choice of 


Sorry, that should be pull_group1_pbcatom. Must remind myself not to 
email before coffee...



Did you mean pull_group2_pbcatom? In my case:

pull_group1_name    = K
pull_group2_name    = CNT

The language for 5.1 pull is (you be the judge on how clear it is):

pull-group1-pbcatom

   (0) The reference atom for the treatment of periodic boundary
   conditions inside the group (this has no effect on the treatment of
   the pbc between groups). This option is only important when the
   diameter of the pull group is larger than half the shortest box
   vector. For determining the COM, all atoms in the group are put at
   their periodic image which is closest topull-group1-pbcatom
   
.
   A value of 0 means that the middle atom (number wise) is used. This
   parameter is not used withpull-group1-geometrycylinder. A value of
   -1 turns on cosine weighting, which is useful for a group of
   molecules in a periodic system,/e.g./a water slab (see Engin et al.
   J. Chem. Phys. B 2010).

Indeed, my group2 is a membrane that is wider than the shortest 
half-box. I am assuming it would be a single atom belonging to the pore 
region...


Thanks,

Alex
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Re: [gmx-users] Regarding minimum size

[Chhavi Yadav]

Hi,

why is calling mdrunner twice a problem?
I get the correct value when mdrunner runs the first time. Why do I get the
error only during the second time considering I am not anyway doing any
settings during both the times?

Thanks,
Chhavi

On Mon, Mar 12, 2018 at 6:24 PM, Mark Abraham 
wrote:

> 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
> > 
> >  

Re: [gmx-users] Regarding minimum size

[Mark Abraham]

Hi,

On Tue, Mar 13, 2018 at 4:11 PM Chhavi Yadav  wrote:

> Hi,
>
> why is calling mdrunner twice a problem?
>

Because nobody wrote the code with that in mind. There's a lot of things
that are built around the assumption that mdrun will start, and then stop,
and nothing happens next.

I get the correct value when mdrunner runs the first time. Why do I get the
> error only during the second time considering I am not anyway doing any
> settings during both the times?
>

I literally have no idea. The only thing I do know is that this is not the
right way to solve your problem "randomly sampling coordinates", but I
don't know enough about what you're trying to do to say anything more
helpful. Is this test particle insertion, or what?

Mark


> Thanks,
> Chhavi
>
> On Mon, Mar 12, 2018 at 6:24 PM, Mark Abraham 
> wrote:
>
> > 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 

Re: [gmx-users] GMX 2018 and 'distance' pull

[Justin Lemkul]

On 3/13/18 10:32 AM, Alex wrote:
It appears that things have improved... I am just glancing and pullf 
and pullx data from the first sample config and both contain only one 
value, even though we set dim to 3D. Does this make sense?




I haven't used the 2018 pull code yet. Presumably this is correct, just 
the distance rather than all its components, though that would be a 
change from previous versions.


-Justin


Thanks,

Alex

On 3/13/2018 8:18 AM, Justin Lemkul wrote:



On 3/13/18 10:17 AM, Alex wrote:

Justin,
You may have a situation that requires manual assignment of 
pull_group1_pbcatom1, as the automatic choice of 


Sorry, that should be pull_group1_pbcatom. Must remind myself not 
to email before coffee...



Did you mean pull_group2_pbcatom? In my case:

pull_group1_name    = K
pull_group2_name    = CNT

The language for 5.1 pull is (you be the judge on how clear it is):

pull-group1-pbcatom 



   (0) The reference atom for the treatment of periodic boundary
   conditions inside the group (this has no effect on the treatment of
   the pbc between groups). This option is only important when the
   diameter of the pull group is larger than half the shortest box
   vector. For determining the COM, all atoms in the group are put at
   their periodic image which is closest topull-group1-pbcatom
. 


   A value of 0 means that the middle atom (number wise) is used. This
   parameter is not used withpull-group1-geometrycylinder. A value of
   -1 turns on cosine weighting, which is useful for a group of
   molecules in a periodic system,/e.g./a water slab (see Engin et al.
   J. Chem. Phys. B 2010).

Indeed, my group2 is a membrane that is wider than the shortest 
half-box. I am assuming it would be a single atom belonging to the 
pore region...




Yes, pull_group2_pbcatom, not 1.

-Justin


Thanks,

Alex






--
==

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] Long Simulations in Batch GMX 2018

[R]

Dear all,

I am doing a simulation of protein of my interest. I could run the simulation 
following the lysozyme tutorial. I am using 2018 version for gromacs.
To start with, I ran the simulation for 1 ns. I want to run long simulation 
though want to make sure that each trajectory files has a manageable size. 
Thus, I would like to run simulation in 5 ns batches i.e.

md_1.trr : 0-5ns
md_2.trr: 5-10ns
md_3.trr: 10-15ns like wise.

I am wondering how to run simulation like this in a loop of 5ns.
Any help would be highly appreciated.

Best,
Roli


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[gmx-users] long simulation in batch

[roli . singh]

Dear all,

I am doing a simulation of protein of my interest. I could run the simulation 
following the lysozyme tutorial. I am using 2018 version for gromacs.
To start with, I ran the simulation for 1 ns. I want to run long simulation 
though want to make sure that each trajectory files has a manageable size. 
Thus, I would like to run simulation in 5 ns batches i.e.

md_1.trr : 0-5ns
md_2.trr: 5-10ns
md_3.trr: 10-15ns like wise.

I am wondering how to run simulation like this in a loop of 5ns.
Any help would be highly appreciated.

Best,
Roli


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Re: [gmx-users] GMX 2018 and 'distance' pull

[Alex]

It's the force on the spring connecting the two groups.

So, then, it's what I said. In any case, I must say that the probe along 
Z was more representative of the reality: a hemispherical slice probes a 
circle near the surface of the membrane, which has nothing to do with 
the pore, but naturally produces a barrier. I wish there was a way to 
probe a spherical symmetry within a given solid angle. If pullf/pullx 
data had any angular info, we could script our own implementation of 
WHAM, but alas.


Alex

code would clarify, because the result of wham now looks rather 
strange -- a long (1.5 nm!) hydration barrier for the ion. Makes 
little physical sense and very different from the bias along Z case.


I am guessing that the sampling of 1 ns per hemispherical slice is 
far from sufficient to probe that space... Just looked at one of the 
trajectories there -- the ion is nowhere near moving around the 
entire slice.


Alex


On 3/13/2018 10:27 AM, Justin Lemkul wrote:



On 3/13/18 10:32 AM, Alex wrote:
It appears that things have improved... I am just glancing and 
pullf and pullx data from the first sample config and both contain 
only one value, even though we set dim to 3D. Does this make sense?




I haven't used the 2018 pull code yet. Presumably this is correct, 
just the distance rather than all its components, though that would 
be a change from previous versions.


-Justin


Thanks,

Alex

On 3/13/2018 8:18 AM, Justin Lemkul wrote:



On 3/13/18 10:17 AM, Alex wrote:

Justin,
You may have a situation that requires manual assignment of 
pull_group1_pbcatom1, as the automatic choice of 


Sorry, that should be pull_group1_pbcatom. Must remind myself 
not to email before coffee...



Did you mean pull_group2_pbcatom? In my case:

pull_group1_name    = K
pull_group2_name    = CNT

The language for 5.1 pull is (you be the judge on how clear it is):

pull-group1-pbcatom 



   (0) The reference atom for the treatment of periodic boundary
   conditions inside the group (this has no effect on the 
treatment of

   the pbc between groups). This option is only important when the
   diameter of the pull group is larger than half the shortest box
   vector. For determining the COM, all atoms in the group are 
put at

   their periodic image which is closest topull-group1-pbcatom
. 

   A value of 0 means that the middle atom (number wise) is used. 
This
   parameter is not used withpull-group1-geometrycylinder. A 
value of

   -1 turns on cosine weighting, which is useful for a group of
   molecules in a periodic system,/e.g./a water slab (see Engin 
et al.

   J. Chem. Phys. B 2010).

Indeed, my group2 is a membrane that is wider than the shortest 
half-box. I am assuming it would be a single atom belonging to 
the pore region...




Yes, pull_group2_pbcatom, not 1.

-Justin


Thanks,

Alex












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Re: [gmx-users] GMX 2018 and 'distance' pull

[Justin Lemkul]

On 3/13/18 4:19 PM, Alex wrote:
What I meant is each of those files now has two columns, the first of 
which is of course time. What the second column is, especially for 
pullf, is a mystery to me. The total radial force? I wish someone who 
wrote the new pull 


It's the force on the spring connecting the two groups.

-Justin

code would clarify, because the result of wham now looks rather 
strange -- a long (1.5 nm!) hydration barrier for the ion. Makes 
little physical sense and very different from the bias along Z case.


I am guessing that the sampling of 1 ns per hemispherical slice is far 
from sufficient to probe that space... Just looked at one of the 
trajectories there -- the ion is nowhere near moving around the entire 
slice.


Alex


On 3/13/2018 10:27 AM, Justin Lemkul wrote:



On 3/13/18 10:32 AM, Alex wrote:
It appears that things have improved... I am just glancing and pullf 
and pullx data from the first sample config and both contain only 
one value, even though we set dim to 3D. Does this make sense?




I haven't used the 2018 pull code yet. Presumably this is correct, 
just the distance rather than all its components, though that would 
be a change from previous versions.


-Justin


Thanks,

Alex

On 3/13/2018 8:18 AM, Justin Lemkul wrote:



On 3/13/18 10:17 AM, Alex wrote:

Justin,
You may have a situation that requires manual assignment of 
pull_group1_pbcatom1, as the automatic choice of 


Sorry, that should be pull_group1_pbcatom. Must remind myself not 
to email before coffee...



Did you mean pull_group2_pbcatom? In my case:

pull_group1_name    = K
pull_group2_name    = CNT

The language for 5.1 pull is (you be the judge on how clear it is):

pull-group1-pbcatom 



   (0) The reference atom for the treatment of periodic boundary
   conditions inside the group (this has no effect on the 
treatment of

   the pbc between groups). This option is only important when the
   diameter of the pull group is larger than half the shortest box
   vector. For determining the COM, all atoms in the group are put at
   their periodic image which is closest topull-group1-pbcatom
. 

   A value of 0 means that the middle atom (number wise) is used. 
This

   parameter is not used withpull-group1-geometrycylinder. A value of
   -1 turns on cosine weighting, which is useful for a group of
   molecules in a periodic system,/e.g./a water slab (see Engin et 
al.

   J. Chem. Phys. B 2010).

Indeed, my group2 is a membrane that is wider than the shortest 
half-box. I am assuming it would be a single atom belonging to the 
pore region...




Yes, pull_group2_pbcatom, not 1.

-Justin


Thanks,

Alex










--
==

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] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?

[Shaun Tung]

unsubscribe

On Tue, Mar 13, 2018 at 1:53 PM, Mark Abraham 
wrote:

> Hi,
>
> I already suggested where to go and find the answer, but you looked
> somewhere else... The PDF you linked is kindly contributed by another user,
> but not official. Anyway, apparently my memory is wrong and you can't do
> what you want. From the reference manual:
>
> If you want to have different functional forms between different groups of
> atoms, this can be set through energy groups. Different tables can be used
> for non-bonded interactions between different energy groups pairs through
> the .mdp option energygrp-table (see details in the User Guide). Atoms that
> should interact with a different potential should be put into different
> energy groups. Between group pairs which are not listed in energygrp-table,
> the normal user tables will be used. This makes it easy to use a different
> functional form between a few types of atoms.
>
> Maybe you want to check out the whole section there. ;-)
>
> Mark
>
> On Tue, Mar 13, 2018 at 5:26 PM Debdas Dhabal 
> wrote:
>
> > Dear Mark,
> >
> > It would be very grateful if you could please comment on my confusion
> > mentioned above.
> >
> > Thank you very much.
> >
> > With regards
> > Debdas
> >
> >
> >
> > On Mon, Mar 12, 2018 at 4:20 PM, Debdas Dhabal 
> > wrote:
> >
> > > 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 <
> mark.j.abra...@gmail.com
> > >
> > > 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 <
> > ddha...@seas.upenn.edu>
> > >> > 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 

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

[Mark Abraham]

Hi,

I already suggested where to go and find the answer, but you looked
somewhere else... The PDF you linked is kindly contributed by another user,
but not official. Anyway, apparently my memory is wrong and you can't do
what you want. From the reference manual:

If you want to have different functional forms between different groups of
atoms, this can be set through energy groups. Different tables can be used
for non-bonded interactions between different energy groups pairs through
the .mdp option energygrp-table (see details in the User Guide). Atoms that
should interact with a different potential should be put into different
energy groups. Between group pairs which are not listed in energygrp-table,
the normal user tables will be used. This makes it easy to use a different
functional form between a few types of atoms.

Maybe you want to check out the whole section there. ;-)

Mark

On Tue, Mar 13, 2018 at 5:26 PM Debdas Dhabal 
wrote:

> Dear Mark,
>
> It would be very grateful if you could please comment on my confusion
> mentioned above.
>
> Thank you very much.
>
> With regards
> Debdas
>
>
>
> On Mon, Mar 12, 2018 at 4:20 PM, Debdas Dhabal 
> wrote:
>
> > 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 <
> ddha...@seas.upenn.edu>
> >> > 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

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue 53

[Mark Abraham]

Hi,

Please don't reply to digests. Please don't subscribe to digests if you
actually want to post and discuss :-)

See figure 3.5, or search for "drift" ;-)

Mark

On Tue, Mar 13, 2018 at 6:28 PM Jo  wrote:

> Hello,
>
> I have looked in the manual and tried the adjustments for
> verlet-buffer-tolerance and rlist (with no sucess), but I did not find a
> plot for this? Can you direct me to this?  I've copied my mdp below if
> anyone could give me some insight.
>
> Thanks,
>
> Jo
>
> RUN PARAMETERS
> integrator   = md
> tinit= 0
> dt   = 0.001
> nsteps   = 1000
> comm-mode= Linear
> nstcomm  = 100
>
> ;OUTPUT PARAMETERS
> nstlog   = 5
> nstenergy= 1
> nstcalcenergy= 100
> nstxout-compressed= 1000
> compressed-x-precision= 1000
>
> ; NEIGHBORLIST PARAMETERS
> cutoff-scheme= Verlet
> nstlist  = 10
> ns_type  = grid
> pbc  = xyz
> verlet-buffer-tolerance  = 5.0e-6 ;-1
>
> ; VDW AND COULOMB PARAMETERS
> coulombtype  = PME
> rcoulomb = 0.9
> coulomb-modifier = Potential-shift
> vdw-type = Cut-off
> rvdw = 0.9
> vdw-modifier = Potential-shift
> table-extension  = 1
>
> ; EWALD PARAMETERS
> fourierspacing   = 0.1
> pme_order= 6
> ewald_rtol   = 1e-06
> ewald_geometry   = 3d
> epsilon_surface  = 0
> DispCorr = EnerPres
>
> ; BAROSTAT AND THERMOSTAT
> Tcoupl   = no ;Nose-hoover
> Pcoupl   = no ;Parrinello-Rahman
> refcoord-scaling = no
>
> ;SETUP VELOCITIES=
> gen_vel  = no
> gen_temp = 298.15
> gen_seed = -1
>
>
>
>
>
>
> >
> > Message: 5
> > Date: Mon, 12 Mar 2018 22:20:45 +
> > From: Mark Abraham 
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] nve simulation
> > Message-ID:
> > 

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

[Debdas Dhabal]

Dear Mark,

Many many thanks for your kind suggestion. I have also gone through the
official Gromacs manual about table potential initially. But I was in a bit
confusion.

Thanks again

Warm regards
Debdas

On Tue, Mar 13, 2018 at 1:53 PM, Mark Abraham 
wrote:

> Hi,
>
> I already suggested where to go and find the answer, but you looked
> somewhere else... The PDF you linked is kindly contributed by another user,
> but not official. Anyway, apparently my memory is wrong and you can't do
> what you want. From the reference manual:
>
> If you want to have different functional forms between different groups of
> atoms, this can be set through energy groups. Different tables can be used
> for non-bonded interactions between different energy groups pairs through
> the .mdp option energygrp-table (see details in the User Guide). Atoms that
> should interact with a different potential should be put into different
> energy groups. Between group pairs which are not listed in energygrp-table,
> the normal user tables will be used. This makes it easy to use a different
> functional form between a few types of atoms.
>
> Maybe you want to check out the whole section there. ;-)
>
> Mark
>
> On Tue, Mar 13, 2018 at 5:26 PM Debdas Dhabal 
> wrote:
>
> > Dear Mark,
> >
> > It would be very grateful if you could please comment on my confusion
> > mentioned above.
> >
> > Thank you very much.
> >
> > With regards
> > Debdas
> >
> >
> >
> > On Mon, Mar 12, 2018 at 4:20 PM, Debdas Dhabal 
> > wrote:
> >
> > > 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 <
> mark.j.abra...@gmail.com
> > >
> > > 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 <
> > ddha...@seas.upenn.edu>
> > >> > 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