Re: [gmx-users] Aggregation or phase separation

[Dallas Warren]

There isn't really anything currently.

It is an issue we deal with, have a few things currently do that are
published. Have another in the works.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 10 October 2017 at 01:08, gozde ergin  wrote:
> I am using Gromacs to study the cis-pinonic acid aggregation in water.
> In order to use the Gibbs-duhem relation, I would like to know if these 
> aggregates form inside the water are pseudo-phase or separate phase?
> Do you have any hint how to define the phase of aggregates in water by using 
> Gromacs tool?
>
> Thanks in advance.
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Re: [gmx-users] Minimization Problem

[Dallas Warren]

Where did you obtain the topology from? What forcefield is it meant to
be used with?  Does that forcefield include bonds between those atom
types?

The error is occurring because when grompp goes through the topology,
it cannot match up the atom types that are bonded together, with an
existing bond within the forcefield.

Easiest solution is to get a topology for that molecule, for the
forcefield you want to use, that someone else has built. Or you could
specify that bonds yourself within the topology.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 10 October 2017 at 04:55, Ednilsom Orestes  wrote:
> Dear Gromacs community
>
> I am trying to run a simulation of choline molecule but found various
> errors concerning to bonds, angles and dihedrals during the minimization.
>
>
>
> Part of the top file (line number in the first column):
> ...
> 29 [ bonds ]
> 30;  aiaj funct
> 311  4 1; N   CT3
> 32114 1; N   CT4
> 331  2 1; N   CT1
> 341  3 1; N   CT2
> 35212 1;   CT1  HC12
> 36213 1;   CT1  HC11
> 37211 1;   CT1  HC13
> 383  7 1;   CT2  HC21
> 393  6 1;   CT2  HC22
> 403  5 1;   CT2  HC23
> 414  8 1;   CT3  HC31
> 42410 1;   CT3  HC32
> 434  9 1;   CT3  HC33
> 44   1417 1;   CT4  HC41
> 45   1415 1;   CT4   CT5
> 46   1416 1;   CT4  HC42
> 47   1520 1;   CT5  HC51
> 48   1518 1;   CT5OH
> 49   1519 1;   CT5  HC52
> 50   2118 1;HOOH
> ...
>
>
> Errors:
>
> ERROR 1 [file topol_choline.top, line 49]:
> No Default Bond type
>
> ERROR 2 [file topol_choline.top, line50]:
> No Default Bond type
>
> and so on with some of the angles and dihedrals...
>
> Does anybody have a clue on how to fix it?
>
> Thanks in advance.
>
> Ednilsom
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[gmx-users] Adding a Mg2+ Dummy model to GROMACS AMBERff03

[Robert König]

Hi,
I am adding a Mg2+ Dummy model to the AMBERff03 FF in GROMACS 2016.3,using the 
paramters from Jiang et al. (given in the supporting material)
http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00286as the newest and "most 
reliable for ATP-Mg2+-Protein conformations".
I was able to implement all parameters except Ai and Bi on page 5/16 in the 
supporting material.Vice versa i am missing the parameters "sigma" and 
"epsilon" for the dummy model in the ffnonbonded.itp file of the FF.
I am not sure how to translate Ai and Bi to "sigma" and "epsilon" and I would 
be glad if someone could help.
If someone did this already I also would be thankful if I could get a record of 
all changes, you did, in the gromacs Amberff03 FF.

Thank you very much,Sincerly,olaf
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Re: [gmx-users] Adding TPO and SEP to amber99sb-ildn.ff - question to aminoacids.hdb entry and "[impropers]" entry in aminoacids.rtp

[Robert König]

Thank you Justin for your review!
I addedTPO 4
1   1   H   N   -C  CA
1   5   HA  CA  N   CB  C
1   5   HB  CB  CA  CG2 OG1
3   4   HG2 CG2 CB  CAandSEP 3
1   1   H   N   -C  CA
1   5   HA  CA  N   CB  C
2   6   HB  CB  CA  OGto aminoacids.hdb. 

That should be right and works.
Sincerly,olaf


 

Justin Lemkul  schrieb am 18:37 Samstag, 7.Oktober 2017:
 

 

On 10/4/17 1:59 PM, Robert König wrote:
> Hi,
> I try to add the two AA SEP and TPO to the AMBER99SB-ILDN FF in GROMACS 
> 2016.3. following the instructions on
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> I added TPO and SEP to aminoacids.rtp like:
> [ TPO ] ; Phosphothreonine from 
> http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_thp.lib
> ; changed: PS=P, OPA=O1P, OPB=O2P, OPC=O3P
>   [ atoms ] ; !entry.THP.unit.atoms table
>   N    N   -0.493700    1
>   H    H    0.301800    2
>      CA    CT  -0.1740  3
>      HA    H1   0.016400    4
>      CB    CT   0.15310 5
>      HB    H1  -0.090900    6
>     CG2    CT  -0.16170 7
>    HG21    HC   0.049600    8
>    HG22    HC   0.049600    9
>    HG23    HC   0.049600   10
>     OG1    OS  -0.637500   11
>   P    P    1.400  12
>     O1P    O2  -0.850  13
>     O2P    O2  -0.850  14
>     O3P    O2  -0.850  15
>   C    C    0.673100   16
>   O    O   -0.585400   17
>   [ bonds ] ; !entry.THP.unit.connectivity table
>   N H
>   N    CA
>      CA    HA
>      CA    CB
>      CA C
>      CB    HB
>      CB   CG2
>      CB   OG1
>     CG2  HG21
>     CG2  HG22
>     CG2  HG23
>     OG1    PS
>   S   O1P
>   S   O2P
>   S   O3P
>   C O
>      -C N   ; is present everywhere else
>   [ impropers ] ; is present everywhere else
>      -C    CA N H
>      CA    +N C O
>
> [ SEP ] ; Phosphoserine from 
> http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_sep.lib
> ; changed: PS=P, OPA=O1P, OPB=O2P, OPC=O3P
>   [ atoms ] ; !entry.SEP.unit.atoms table
>   N    N   -0.493700    1
>   H    H    0.301800    2
>      CA    CT  -0.238000    3
>      HA    H1   0.093700    4
>      CB    CT   0.078200    5
>     HB2    H1  -0.060200    6
>     HB3    H1  -0.060200    7
>      OG    OS  -0.559300    8
>   P    P    1.4 9
>     O1P    O2  -0.850  10
>     O2P    O2  -0.850  11
>     O3P    O2  -0.850  12
>   C    C    0.673100   13
>   O    O   -0.585400   14
>   [ bonds ] ; !entry.THP.unit.connectivity table
>   N H
>   N    CA
>      CA    HA
>      CA    CB
>      CA C
>      CB   HB2
>      CB   HB3
>      CB    OG
>      OG    PS
>   S   O1P
>   S   O2P
>   S   O3P
>   C O
>      -C N   ; is present everywhere else
>   [ impropers ] ; is present everywhere else
>      -C    CA N H
>      CA    +N C O
> My first question is, like I commented, on both entries the last four lines 
> are not in the parameters I got from
> http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_thp.lib
>  and
> http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_sep.libbut
>  are found on all the other entries.So do I need these lines, are they right 
> that way and what does it mean?

The functional form uses improper dihedrals to maintain planarity of the 
peptide bond. This may or may not be explicitly in every force field's 
files, or may be in places you're not looking.

The "-C N" line indicates that there's a bond between the preceding (-) 
residue and this one. GROMACS uses +/- connectivity to indicate bonds 
between residues in a chain.

> Second is in aminoacid.hdb.The entries look like:
> "THR    5"
> 1    1    H    N    -C    CA
> 1    5    HA    CA    N    CB    C
> 1    5    HB    CB    CA    CG2    OG1
> 3    4    HG2    CG2    CB    CA
> 1    2    HG1    OG1    CB    CA
> So I added till now:
> TPO 4
> 1   H
> 1   HA
> 1   HB
> 3   HG2
> SEP 4
> 1   H
> 1   HA
> 1   HB2
> 1   HB3
> is this right that far, especially TPO with 4 lines and 3 HG2?If somebody 
> added these AA already I would be

Looks fine (assuming you've got the rest of those lines complete and not 
just this skeleton).

-Justin

> grateful for the missing parameters or a reliable source, I am not sure that 
> my own estimations will be totally right.
> Thanks a lot!
> If you are still in good mood I would be very 

[gmx-users] Minimization Problem

[Ednilsom Orestes]

Dear Gromacs community

I am trying to run a simulation of choline molecule but found various
errors concerning to bonds, angles and dihedrals during the minimization.



Part of the top file (line number in the first column):
...
29 [ bonds ]
30;  aiaj funct
311  4 1; N   CT3
32114 1; N   CT4
331  2 1; N   CT1
341  3 1; N   CT2
35212 1;   CT1  HC12
36213 1;   CT1  HC11
37211 1;   CT1  HC13
383  7 1;   CT2  HC21
393  6 1;   CT2  HC22
403  5 1;   CT2  HC23
414  8 1;   CT3  HC31
42410 1;   CT3  HC32
434  9 1;   CT3  HC33
44   1417 1;   CT4  HC41
45   1415 1;   CT4   CT5
46   1416 1;   CT4  HC42
47   1520 1;   CT5  HC51
48   1518 1;   CT5OH
49   1519 1;   CT5  HC52
50   2118 1;HOOH
...


Errors:

ERROR 1 [file topol_choline.top, line 49]:
No Default Bond type

ERROR 2 [file topol_choline.top, line50]:
No Default Bond type

and so on with some of the angles and dihedrals...

Does anybody have a clue on how to fix it?

Thanks in advance.

Ednilsom
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Re: [gmx-users] shift the LJ potential

[Faezeh Pousaneh]

Hi Mark,

I have a given function for pseudo hard-sphere potential, which has
different powers than LJ and a constant. I have to insert the constant in
order to properly define the cut-off for my hard spheres.
I just realized that I can use "user-specified potential". I guess I can
include the constant there, yes?

One more thing, I need to have my own particles, spheres with a diameter
"a". How can I have them in gromacs?

On Oct 9, 2017 3:44 PM, "Mark Abraham"  wrote:

Hi,

Shifting the potential doesn't affect the sampling - only the forces do.
How does that affect what you're thinking of?

Mark

On Mon, Oct 9, 2017 at 3:14 PM Faezeh Pousaneh  wrote:

> Hi,
>
> I would like to shift the LJ interaction between my particle by a
constant,
> (to remove attraction), how can I change the function?
>
>
> Best regards
> --
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[gmx-users] Local Coordinates with DomDec

[Bradley Treece]

Hi All,

I have a question about the handling of coordinates in local arrays with
domain decomposition. It may take a moment to get to my actual question,
but I want to make sure to be thorough with my explanation. Also, if I need
to point this question toward a different mailing list, please let me know.

By referencing the data structure reference page, I am aware that the
mdatoms structure contains nr and homenr indicating the number of local and
home atoms dealt with in the arrays x, f, and etc. I also know how to use
the commrec to get back the global indices. This part may not be crucial to
my question, but I also would like to check that I have this right. I
searched high and low for the mdatoms->start integer but couldn't find it
anywhere. I assume, and through careful checks, feel confident that this is
part of an older version and it is the case that home atoms are contained
in the first homenr atoms of an array; meaning the start parameter was
somehow tied to the location of home atoms in the arrays but is now
obsolete.

My question is in regard to local atoms that are not part of the home set.
Many of the position and force values for these behave as expected, but
occasionally the three vectors for both are only zeros (almost as if they
were uninitialized). I know for topological reasons that these atoms should
not have coordinates of zero and presume that their forces should not be
zero. I also have verified that they do fall below the nr cutoff of the
index. I was wondering if anyone could point me to why this might be the
case or correct any misunderstanding I have for how domdec manages these
things.

For reference, most of my testing takes place within the do_force function
of src/gromacs/mdlib/sim_util.cpp  but I have done some checks elsewhere in
the code to verify that it is not an issue isolated to this part of the
code. I am also running 5.1.1 in case there are any version dependencies to
take into account.

Thanks for your help,

Bradley Treece
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[gmx-users] Aggregation or phase separation

[gozde ergin]

I am using Gromacs to study the cis-pinonic acid aggregation in water.
In order to use the Gibbs-duhem relation, I would like to know if these 
aggregates form inside the water are pseudo-phase or separate phase?
Do you have any hint how to define the phase of aggregates in water by using 
Gromacs tool?

Thanks in advance.
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Re: [gmx-users] shift the LJ potential

[Mark Abraham]

Hi,

Shifting the potential doesn't affect the sampling - only the forces do.
How does that affect what you're thinking of?

Mark

On Mon, Oct 9, 2017 at 3:14 PM Faezeh Pousaneh  wrote:

> Hi,
>
> I would like to shift the LJ interaction between my particle by a constant,
> (to remove attraction), how can I change the function?
>
>
> Best regards
> --
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[gmx-users] shift the LJ potential

[Faezeh Pousaneh]

Hi,

I would like to shift the LJ interaction between my particle by a constant,
(to remove attraction), how can I change the function?


Best regards
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[gmx-users] not specific molecule or atom

[Faezeh Pousaneh]

Hi

I am trying to simulate 'sphere particles' with a diameters with specific
interactions among them. How can I have my own particles not a defined
molecules or atoms in the force fields.

thanks for answer,
Best regards
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[gmx-users] problems with difference in the COM distances in US sampling

[ABEL Stephane]

Hello 

I am trying to perform some US calculations to obtain the potential of mean 
force of the insertion of a molecule inside a lipid bilayer. For that I follow 
the tutorial of Dr Justin Lemkul with some modifications and start the 
simulations with the following mdp 

pull_group1_name= MEMB
pull_group2_name= FEI
pull_ngroups= 2
pull_ncoords= 1
pull-nstxout= 500
pull-nstfout= 500
pull_print_com1 = yes
pull_print_ref-value= yes
;pull_print_components   = yes
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple direction decrease
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_k = 1500
;pull_coord1_rate= -0.01
pull_coord1_start   = yes 

And indeed after 800 ps the molecule move to the bilayer center and  the 
distance between the COMs of the molecule and the bilayer reported in the pullx 
file is close 0 nm. 

However when I do the second step of the tutorial with the perl script provide 
in the  J. lemkul tutorial (perl_distance.pl) to select the US windows, the 
distance is greater than around 1 for the same config . see below

the pullx = 

800.0.00105624  -4.02734

the COM-distance computed with perl script  after the membrane was centered in 
the box with -pbc mol is 

800 1.264

Why  this difference, and to choose the good interval for the US sampling

I use the following command trough the perl script 

distance_PMF$ gmx_mpi distance -s 
./US_Files_step1/PHE_POPC_Memb_CHARMM_PMF_1500Kj_01rate_US_step1.tpr -f 
conf800.gro -n System.ndx -oall dist0.xvg -select 'com of group MEMB plus com 
of group FEI'



Thank you in advance

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