date:20180114




On 1/14/18 12:35 PM, rose rahmani wrote:

Yes.
thank you so much

On Sun, Jan 14, 2018 at 7:05 PM, Justin Lemkul  wrote:



On 1/14/18 9:59 AM, rose rahmani wrote:


Hello;

this is md_pull.mdp

integrator   = md
dt   = 0.002
nsteps   = 100
nstxout  = 5000
nstvout  = 5000
nstfout  = 500
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
nstlist  = 10
rlist= 1.5
cutoff-scheme= Verlet
energygrp-excl   = WAL WAL ZnS ZnS
coulombtype  = pme
rcoulomb = 1.2
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen_vel  = no
constraints  = h-bonds
ns_type  = grid
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrps   = SOL WAL ZnS Protein NA CL
energygrp-excl   = WAL WAL ZnS ZnS
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= ZnS
pull_group2_name= Protein
pull_coord1_type= umbrella
pull_coord1_geometry= direction
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_vec = 0 0 1
pull_coord1_rate= -0.001
pull_coord1_k   = 5000
pull_coord1_start   = yes
pull_nstxout= 10

--

ERROR 1 [file md_pull.mdp]:
Energy group exclusions are not (yet) implemented for the Verlet scheme


WARNING 1 [file md_pull.mdp]:
Can not exclude the lattice Coulomb energy between energy groups

Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.208 nm, buffer size 0.008 nm
Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 36x36x300, spacing 0.111 0.111 0.120
Pull group  natoms  pbc atom  distance at start  reference at t=0
 1   560   280
 226   773   1.763 nm  1.763 nm
Estimate for the relative computational load of the PME mesh part: 0.77

NOTE 3 [file md_pull.mdp]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off and the PME grid spacing.


This run will generate roughly 149 Mb of data

There were 3 notes

There was 1 warning

There were 3 notes

There was 1 warning

---
Program gmx grompp, VERSION 5.1.4
Source code file:
/home/sjalili/gromacs-5.1.4/src/gromacs/gmxpreprocess/grompp.c, line:
2107

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

i implemented  energygr-excl in mdp file, so why get this error?!


Read the above - such exclusions are not compatible with either the Verlet
scheme or with PME.

Sorry, i couldn't understand "Read the above -such exclusions " ?


Read the messages above (error 1 and warning 1) as they tell you 
precisely why things fail. Energy group exclusions are not compatible 
with either Verlet or PME.


-Justin


and my second question is that i want to pull Protein(to get closer to

sheet) to ZnS sheet, so should i use position restraint for Protein in
this
step?


If you want to induce motion in some species, does it make sense to apply
a biasing potential that prevents motion?

and what is the difference between geometry= direction or distance in my

system?


Please see the manual for a description of these features.

-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] Problem fpr building a peptide with two modified residues with amber ff




On 1/14/18 12:04 PM, ABEL Stephane wrote:

Thank you, Justin for your interest to my problem,

But even if I use the -missing argument*, pdb2gmx still wants to add an Nter 
ILE instead of a central a simple ILE :((


Ile should not be treated as a terminal residue, and it wasn't in the 
screen output you provided before after adding your custom residues to 
residuetypes.dat. That's a prerequisite if you want anything to work. 
Getting the connectivity right after dealing with the custom residues is 
the next problem after that.


-Justin


*gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
Atosiban_amber14sb.pdb -i Atosiban_posre.itp -missing

I will try to search a workaround

Best

Stéphane


De : ABEL Stephane
Envoy? : dimanche 14 janvier 2018 16:52
? : gromacs.org_gmx-users@maillist.sys.kth.se
Objet : RE:gromacs.org_gmx-users Digest, Vol 165, Issue 50

Thanks Justin

First I forgot to say that I am building a cyclic peptide (Atosiban, 
https://fr.wikipedia.org/wiki/Atosiban). I construct two RTP for the  MER 
(3-Mercaptopropionyl-) and TYO (ethoxy tyrosine. And they are correct since the 
two residues are well constructed and linked together with pdb2gmx as it is 
shown If I consider the ILE as NILE

For linking the MER and CYX I define a bond with the specbond.dat (the 
corresponding bond is shown in the  pdb2gmx output). The only problem I have is 
that NILE residue is chosen instead of ILE

How to resolve this problem and to force pdb2gmx to use ILE ? It is strange or 
I found a subtle error I cannot find.

St?phane




--

Message: 3
Date: Sun, 14 Jan 2018 10:34:08 -0500
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem fpr building a peptide with two
 modified residues with amber ff
Message-ID: <541ddbd0-378e-16eb-79a4-f161235d4...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 1/14/18 10:04 AM, ABEL Stephane wrote:

Hi Justin

I have added the TYO and MER residue as Protein is the residuetypes.dat. And 
the the following output with pdb2gmx. I select 2 and 6

##
gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes


Select the Force Field:
  From '/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top/':
   1: Amber12sb ff99SB + new backbone and side chain torsion for protein
   2: AMBER14SB_parmbsc1 (ff14SB for protein + parmbsc1 for DNA)
   3: AMBER94 BCL force field (J. Comp. Chem. 2012, 33, 1969?1980)
   4: CHARMM36 all-atom force field (July 2017)
   5: CHARMM36 all-atom force field, surfactants and pigments
   6: GLYCAM06 force field for alkylglycosides and RG1 (2011, J. Phys. Chem. B 
2011, 115, 487-499 )
   7: GROMOS96 2016H66 force field (J. Chem. Theory. Comput., 2016, 12, 
3825?3850)
   8: GROMOS96 53a6 force field with PVP (JCC 2004 vol 25 pag 1656 and J. Phys. 
Chem. C, 2015, 119 (14), pp 7888?7899)
   9: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 
10.1002/jcc.21675)
10: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
  From '/ccc/products/gromacs-5.1.2/default/share/gromacs/top':
11: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
12: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
13: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
461-469, 1996)
14: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
1049-1074, 2000)
15: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
2006)
16: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
78, 1950-58, 2010)
17: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
18: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
19: GROMOS96 43a1 force field
20: GROMOS96 43a2 force field (improved alkane dihedrals)
21: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
22: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
23: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
24: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
25: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
2

Using the Amber14sb_parmbsc1 force field in directory 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff

Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/watermodels.dat

Select the Water Model:
   1: TIP3P TIP 3-point, recommended
   2: TIP4P TIP 4-point
   3: TIP4P-Ew  TIP 4-point optimized with Ewald
   4: SPC   simple point charge
   5: SPC/E extended simple point charge
   6: None
6
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.r2b

Re: [gmx-users] energy group exclusion

2018-01-14 Thread rose rahmani

Yes.
thank you so much

On Sun, Jan 14, 2018 at 7:05 PM, Justin Lemkul  wrote:

>
>
> On 1/14/18 9:59 AM, rose rahmani wrote:
>
>> Hello;
>>
>> this is md_pull.mdp
>>
>> integrator   = md
>> dt   = 0.002
>> nsteps   = 100
>> nstxout  = 5000
>> nstvout  = 5000
>> nstfout  = 500
>> nstlog   = 500
>> nstenergy= 1000
>> nstxtcout= 1000
>> nstlist  = 10
>> rlist= 1.5
>> cutoff-scheme= Verlet
>> energygrp-excl   = WAL WAL ZnS ZnS
>> coulombtype  = pme
>> rcoulomb = 1.2
>> vdwtype  = Switch
>> rvdw_switch  = 1.0
>> rvdw = 1.2
>> pcoupl   = no
>> gen_vel  = no
>> constraints  = h-bonds
>> ns_type  = grid
>> pbc  = xy
>> freezegrps   = WAL ZnS
>> freezedim= Y Y Y Y Y Y
>> energygrps   = SOL WAL ZnS Protein NA CL
>> energygrp-excl   = WAL WAL ZnS ZnS
>> nwall= 2
>> wall-atomtype= C C
>> wall-type= 9-3
>> wall-density = 150 150
>> wall-ewald-zfac  = 3
>> ewald-geometry   = 3dc
>> fourierspacing   = 0.12
>> tcoupl   = v-rescale
>> tc-grps  = System
>> tau-t= 0.1
>> ref-t= 300
>>
>> ; Pull code
>> pull= yes
>> pull_ngroups= 2
>> pull_ncoords= 1
>> pull_group1_name= ZnS
>> pull_group2_name= Protein
>> pull_coord1_type= umbrella
>> pull_coord1_geometry= direction
>> pull_coord1_groups  = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_vec = 0 0 1
>> pull_coord1_rate= -0.001
>> pull_coord1_k   = 5000
>> pull_coord1_start   = yes
>> pull_nstxout= 10
>>
>> --
>>
>> ERROR 1 [file md_pull.mdp]:
>>Energy group exclusions are not (yet) implemented for the Verlet scheme
>>
>>
>> WARNING 1 [file md_pull.mdp]:
>>Can not exclude the lattice Coulomb energy between energy groups
>>
>> Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
>> Calculated rlist for 1x1 atom pair-list as 1.208 nm, buffer size 0.008 nm
>> Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
>> Note that mdrun will redetermine rlist based on the actual pair-list setup
>> Calculating fourier grid dimensions for X Y Z
>> Using a fourier grid of 36x36x300, spacing 0.111 0.111 0.120
>> Pull group  natoms  pbc atom  distance at start  reference at t=0
>> 1   560   280
>> 226   773   1.763 nm  1.763 nm
>> Estimate for the relative computational load of the PME mesh part: 0.77
>>
>> NOTE 3 [file md_pull.mdp]:
>>The optimal PME mesh load for parallel simulations is below 0.5
>>and for highly parallel simulations between 0.25 and 0.33,
>>for higher performance, increase the cut-off and the PME grid spacing.
>>
>>
>> This run will generate roughly 149 Mb of data
>>
>> There were 3 notes
>>
>> There was 1 warning
>>
>> There were 3 notes
>>
>> There was 1 warning
>>
>> ---
>> Program gmx grompp, VERSION 5.1.4
>> Source code file:
>> /home/sjalili/gromacs-5.1.4/src/gromacs/gmxpreprocess/grompp.c, line:
>> 2107
>>
>> Fatal error:
>> There was 1 error in input file(s)
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>>
>> i implemented  energygr-excl in mdp file, so why get this error?!
>>
>
> Read the above - such exclusions are not compatible with either the Verlet
> scheme or with PME.

Sorry, i couldn't understand "Read the above -such exclusions " ?

> and my second question is that i want to pull Protein(to get closer to
>> sheet) to ZnS sheet, so should i use position restraint for Protein in
>> this
>> step?
>>
>
> If you want to induce motion in some species, does it make sense to apply
> a biasing potential that prevents motion?
>
> and what is the difference between geometry= direction or distance in my
>> system?
>>
>
> Please see the manual for a description of these features.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff

Thank you, Justin for your interest to my problem, 

But even if I use the -missing argument*, pdb2gmx still wants to add an Nter 
ILE instead of a central a simple ILE :((

*gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
Atosiban_amber14sb.pdb -i Atosiban_posre.itp -missing

I will try to search a workaround 

Best 

Stéphane


De : ABEL Stephane
Envoy? : dimanche 14 janvier 2018 16:52
? : gromacs.org_gmx-users@maillist.sys.kth.se
Objet : RE:gromacs.org_gmx-users Digest, Vol 165, Issue 50

Thanks Justin

First I forgot to say that I am building a cyclic peptide (Atosiban, 
https://fr.wikipedia.org/wiki/Atosiban). I construct two RTP for the  MER 
(3-Mercaptopropionyl-) and TYO (ethoxy tyrosine. And they are correct since the 
two residues are well constructed and linked together with pdb2gmx as it is 
shown If I consider the ILE as NILE

For linking the MER and CYX I define a bond with the specbond.dat (the 
corresponding bond is shown in the  pdb2gmx output). The only problem I have is 
that NILE residue is chosen instead of ILE

How to resolve this problem and to force pdb2gmx to use ILE ? It is strange or 
I found a subtle error I cannot find.

St?phane




--

Message: 3
Date: Sun, 14 Jan 2018 10:34:08 -0500
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem fpr building a peptide with two
modified residues with amber ff
Message-ID: <541ddbd0-378e-16eb-79a4-f161235d4...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 1/14/18 10:04 AM, ABEL Stephane wrote:
> Hi Justin
>
> I have added the TYO and MER residue as Protein is the residuetypes.dat. And 
> the the following output with pdb2gmx. I select 2 and 6
>
> ##
>gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
> Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes
>
>
> Select the Force Field:
>  From '/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top/':
>   1: Amber12sb ff99SB + new backbone and side chain torsion for protein
>   2: AMBER14SB_parmbsc1 (ff14SB for protein + parmbsc1 for DNA)
>   3: AMBER94 BCL force field (J. Comp. Chem. 2012, 33, 1969?1980)
>   4: CHARMM36 all-atom force field (July 2017)
>   5: CHARMM36 all-atom force field, surfactants and pigments
>   6: GLYCAM06 force field for alkylglycosides and RG1 (2011, J. Phys. Chem. B 
> 2011, 115, 487-499 )
>   7: GROMOS96 2016H66 force field (J. Chem. Theory. Comput., 2016, 12, 
> 3825?3850)
>   8: GROMOS96 53a6 force field with PVP (JCC 2004 vol 25 pag 1656 and J. 
> Phys. Chem. C, 2015, 119 (14), pp 7888?7899)
>   9: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 
> 10.1002/jcc.21675)
> 10: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
> 10.1007/s00249-011-0700-9)
>  From '/ccc/products/gromacs-5.1.2/default/share/gromacs/top':
> 11: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
> 1999-2012, 2003)
> 12: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
> 13: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
> 461-469, 1996)
> 14: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
> 1049-1074, 2000)
> 15: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
> 2006)
> 16: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
> 78, 1950-58, 2010)
> 17: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
> 18: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
> 19: GROMOS96 43a1 force field
> 20: GROMOS96 43a2 force field (improved alkane dihedrals)
> 21: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> 22: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> 23: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 24: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
> 10.1007/s00249-011-0700-9)
> 25: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 2
>
> Using the Amber14sb_parmbsc1 force field in directory 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff
>
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/watermodels.dat
>
> Select the Water Model:
>   1: TIP3P TIP 3-point, recommended
>   2: TIP4P TIP 4-point
>   3: TIP4P-Ew  TIP 4-point optimized with Ewald
>   4: SPC   simple point charge
>   5: SPC/E extended simple point charge
>   6: None
> 6
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.r2b
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.r2b
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.r2b
> Reading

Re: [gmx-users] rlist

Thanks a lot,


Best regards


On Sun, Jan 14, 2018 at 5:32 PM, Justin Lemkul  wrote:

>
>
> On 1/14/18 11:29 AM, Faezeh Pousaneh wrote:
>
>> Thank you Justin, now I understood. However, I do not have any target data
>> for my system. What do you suggest? the longer rcoulomb is safer, right?
>>
>
> Not necessarily. Longer cutoffs do not imply greater accuracy, nor does
> any specific value. It depends on your model. You have to demonstrate to a
> skeptical audience that your methods are sound. That requires describing a
> known system and its structure, energetics, and dynamics. Then you can move
> to predicting unknowns. Without that, there's no control to determine if
> your work is meaningful or a random number generator.
>
>
> -Justin
>
>
>> Best regards
>>
>>
>> On Sun, Jan 14, 2018 at 4:47 PM, Justin Lemkul  wrote:
>>
>>
>>> On 1/14/18 10:42 AM, Faezeh Pousaneh wrote:
>>>
>>> Thanks Justin. But I only define vdW potential form, coulomb potential
 form
 is as in Gromacs. So I would like to have electrostatic interactions as
 other systems, so are

 rlist = 0.9  (in nm)
 rcoulomb= 0.9  (in nm)

 fine while I am using PME?

 Again, there is no standard value here and it is dictated by the
>>> functional form being used. You have a custom interaction potential, even
>>> if you're using normal PME alongside you have user-defined, tabulated vdW
>>> interactions. Presumably there should be some evaluation of what cutoffs
>>> are used to satisfy whatever the assumptions are in the parametrization
>>> of
>>> your model, i.e. you need to have some target data of a known system that
>>> tells you that your physical model (cutoffs and functional form) is
>>> right,
>>> and then you use those same settings in whatever systems are of interest.
>>>
>>> -Justin
>>>
>>>
>>> Best regards
>>>

 On Sun, Jan 14, 2018 at 3:46 PM, Justin Lemkul  wrote:


 On 1/14/18 6:01 AM, Faezeh Pousaneh wrote:
>
> Hi,
>
>> I have a system of charged hard spheres (user-potential), where the
>> vdW
>> cut-off should be diameter of my molecule 0.3479. I wonder if I chose
>> rlist
>> and rcoulomb correctly? (see below please)
>>
>> I'm not sure if anyone can tell you that. You're using custom
>>
> potentials,
> so setting cutoffs is part of the parametrization of that potential
> itself.
>
> -Justin
>
>
> integrator= md
>
> dt= 0.001
>> nsteps= 3000
>> nstxout   = 10   ; save coordinates
>> every 0
>> ps
>> nstvout   = 10   ; save velocities
>> every
>> 0
>> ps
>> nstlog= 10   ; update log file
>> every
>> nstenergy = 10; save energies every
>> nstxtcout = 10   ; Output frequency for
>> xtc
>> file
>> xtc-precision = 10   ; precision for xtc file
>> ns_type   = grid; search neighboring grid
>> cells
>> nstlist   = 10   ;  fs
>> pbc   = xyz ; 3-D PBC
>> rlist  = 0.9 ; short-range
>> neighbor-list
>> cutoff (in nm)
>> rcoulomb  = 0.9 ; short-range
>> electrostatic
>> cutoff
>> (in nm)
>> rvdw  = 0.3479  ; short-range van der
>> Waals
>> cutoff
>> (in nm)
>> coulombtype   = PME-user ; Particle Mesh Ewald
>> for
>> long-range electrostatics
>> pme_order = 4   ; cubic interpolation
>> fourierspacing= 0.16; grid spacing for FFT
>> vdw-type  = user
>> Tcoupl= berendsen   ; modified Berendsen
>> thermostat
>> tc-grps   = co2   rest   ; two coupling
>> groups -
>> more accurate
>> tau_t =  0.1   0.1 ; time constant, in ps
>> ref_t =  179.8  179.8 ; reference temperature,
>> one
>> for
>> each group, in K
>> ;tc-grps  = system
>> cutoff-scheme  =group
>> energygrps= co2 rest
>> Pcoupl=  berendsen ;Parrinello-Rahman
>> Pcoupltype= Isotropic
>> tau_p = 1.0
>> compressibility   = 6.2e-5
>> ref_p = 5500.0
>> gen_vel   = yes
>> gen_temp  = 179.8
>> gen_seed  = 712349
>>

Re: [gmx-users] rlist




On 1/14/18 11:29 AM, Faezeh Pousaneh wrote:

Thank you Justin, now I understood. However, I do not have any target data
for my system. What do you suggest? the longer rcoulomb is safer, right?


Not necessarily. Longer cutoffs do not imply greater accuracy, nor does 
any specific value. It depends on your model. You have to demonstrate to 
a skeptical audience that your methods are sound. That requires 
describing a known system and its structure, energetics, and dynamics. 
Then you can move to predicting unknowns. Without that, there's no 
control to determine if your work is meaningful or a random number 
generator.


-Justin



Best regards


On Sun, Jan 14, 2018 at 4:47 PM, Justin Lemkul  wrote:



On 1/14/18 10:42 AM, Faezeh Pousaneh wrote:


Thanks Justin. But I only define vdW potential form, coulomb potential
form
is as in Gromacs. So I would like to have electrostatic interactions as
other systems, so are

rlist = 0.9  (in nm)
rcoulomb= 0.9  (in nm)

fine while I am using PME?


Again, there is no standard value here and it is dictated by the
functional form being used. You have a custom interaction potential, even
if you're using normal PME alongside you have user-defined, tabulated vdW
interactions. Presumably there should be some evaluation of what cutoffs
are used to satisfy whatever the assumptions are in the parametrization of
your model, i.e. you need to have some target data of a known system that
tells you that your physical model (cutoffs and functional form) is right,
and then you use those same settings in whatever systems are of interest.

-Justin


Best regards


On Sun, Jan 14, 2018 at 3:46 PM, Justin Lemkul  wrote:



On 1/14/18 6:01 AM, Faezeh Pousaneh wrote:

Hi,

I have a system of charged hard spheres (user-potential), where the vdW
cut-off should be diameter of my molecule 0.3479. I wonder if I chose
rlist
and rcoulomb correctly? (see below please)

I'm not sure if anyone can tell you that. You're using custom

potentials,
so setting cutoffs is part of the parametrization of that potential
itself.

-Justin


integrator= md


dt= 0.001
nsteps= 3000
nstxout   = 10   ; save coordinates
every 0
ps
nstvout   = 10   ; save velocities every
0
ps
nstlog= 10   ; update log file every
nstenergy = 10; save energies every
nstxtcout = 10   ; Output frequency for xtc
file
xtc-precision = 10   ; precision for xtc file
ns_type   = grid; search neighboring grid
cells
nstlist   = 10   ;  fs
pbc   = xyz ; 3-D PBC
rlist  = 0.9 ; short-range
neighbor-list
cutoff (in nm)
rcoulomb  = 0.9 ; short-range electrostatic
cutoff
(in nm)
rvdw  = 0.3479  ; short-range van der Waals
cutoff
(in nm)
coulombtype   = PME-user ; Particle Mesh Ewald
for
long-range electrostatics
pme_order = 4   ; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT
vdw-type  = user
Tcoupl= berendsen   ; modified Berendsen
thermostat
tc-grps   = co2   rest   ; two coupling
groups -
more accurate
tau_t =  0.1   0.1 ; time constant, in ps
ref_t =  179.8  179.8 ; reference temperature,
one
for
each group, in K
;tc-grps  = system
cutoff-scheme  =group
energygrps= co2 rest
Pcoupl=  berendsen ;Parrinello-Rahman
Pcoupltype= Isotropic
tau_p = 1.0
compressibility   = 6.2e-5
ref_p = 5500.0
gen_vel   = yes
gen_temp  = 179.8
gen_seed  = 712349
DispCorr  =no;  EnerPres; account for cut-off vdW
scheme
constraints   = all-bonds   ; all bonds constrained
(fixed
length)
continuation  = no ; Restarting after NPT
constraint-algorithm  =  lincs   ; holonomic constraints
lincs_iter= 1   ; accuracy of LINCS
lincs_order   = 4   ; also related to accuracy
Best regards

--

==

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

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

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

==

--
Gromacs

Re: [gmx-users] rlist

Thank you Justin, now I understood. However, I do not have any target data
for my system. What do you suggest? the longer rcoulomb is safer, right?


Best regards


On Sun, Jan 14, 2018 at 4:47 PM, Justin Lemkul  wrote:

>
>
> On 1/14/18 10:42 AM, Faezeh Pousaneh wrote:
>
>> Thanks Justin. But I only define vdW potential form, coulomb potential
>> form
>> is as in Gromacs. So I would like to have electrostatic interactions as
>> other systems, so are
>>
>>rlist = 0.9  (in nm)
>>rcoulomb= 0.9  (in nm)
>>
>> fine while I am using PME?
>>
>
> Again, there is no standard value here and it is dictated by the
> functional form being used. You have a custom interaction potential, even
> if you're using normal PME alongside you have user-defined, tabulated vdW
> interactions. Presumably there should be some evaluation of what cutoffs
> are used to satisfy whatever the assumptions are in the parametrization of
> your model, i.e. you need to have some target data of a known system that
> tells you that your physical model (cutoffs and functional form) is right,
> and then you use those same settings in whatever systems are of interest.
>
> -Justin
>
>
> Best regards
>>
>>
>> On Sun, Jan 14, 2018 at 3:46 PM, Justin Lemkul  wrote:
>>
>>
>>> On 1/14/18 6:01 AM, Faezeh Pousaneh wrote:
>>>
>>> Hi,

 I have a system of charged hard spheres (user-potential), where the vdW
 cut-off should be diameter of my molecule 0.3479. I wonder if I chose
 rlist
 and rcoulomb correctly? (see below please)

 I'm not sure if anyone can tell you that. You're using custom
>>> potentials,
>>> so setting cutoffs is part of the parametrization of that potential
>>> itself.
>>>
>>> -Justin
>>>
>>>
>>> integrator= md
>>>
dt= 0.001
nsteps= 3000
nstxout   = 10   ; save coordinates
 every 0
 ps
nstvout   = 10   ; save velocities every
 0
 ps
nstlog= 10   ; update log file every
nstenergy = 10; save energies every
nstxtcout = 10   ; Output frequency for xtc
 file
xtc-precision = 10   ; precision for xtc file
ns_type   = grid; search neighboring grid
 cells
nstlist   = 10   ;  fs
pbc   = xyz ; 3-D PBC
rlist  = 0.9 ; short-range
 neighbor-list
 cutoff (in nm)
rcoulomb  = 0.9 ; short-range electrostatic
 cutoff
 (in nm)
rvdw  = 0.3479  ; short-range van der Waals
 cutoff
 (in nm)
coulombtype   = PME-user ; Particle Mesh Ewald
 for
 long-range electrostatics
pme_order = 4   ; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT
vdw-type  = user
Tcoupl= berendsen   ; modified Berendsen
 thermostat
tc-grps   = co2   rest   ; two coupling
 groups -
 more accurate
tau_t =  0.1   0.1 ; time constant, in ps
ref_t =  179.8  179.8 ; reference temperature,
 one
 for
 each group, in K
;tc-grps  = system
 cutoff-scheme  =group
energygrps= co2 rest
Pcoupl=  berendsen ;Parrinello-Rahman
Pcoupltype= Isotropic
tau_p = 1.0
compressibility   = 6.2e-5
ref_p = 5500.0
gen_vel   = yes
gen_temp  = 179.8
gen_seed  = 712349
DispCorr  =no;  EnerPres; account for cut-off vdW
 scheme
constraints   = all-bonds   ; all bonds constrained
 (fixed
 length)
continuation  = no ; Restarting after NPT
constraint-algorithm  =  lincs   ; holonomic constraints
lincs_iter= 1   ; accuracy of LINCS
lincs_order   = 4   ; also related to accuracy
 Best regards

 --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue 50




On 1/14/18 10:52 AM, ABEL Stephane wrote:

Thanks Justin

First I forgot to say that I am building a cyclic peptide (Atosiban, 
https://fr.wikipedia.org/wiki/Atosiban). I construct two RTP for the  MER 
(3-Mercaptopropionyl-) and TYO (ethoxy tyrosine. And they are correct since the 
two residues are well constructed and linked together with pdb2gmx as it is 
shown If I consider the ILE as NILE

For linking the MER and CYX I define a bond with the specbond.dat (the 
corresponding bond is shown in the  pdb2gmx output). The only problem I have is 
that NILE residue is chosen instead of ILE

How to resolve this problem and to force pdb2gmx to use ILE ? It is strange or 
I found a subtle error I cannot find.


I've never dealt with cyclic peptides in GROMACS and most threads about 
them tend to die off without resolution. It's not something pdb2gmx does 
well. Presumably you could use the -missing flat (very dangerous!) and 
then verify that the topology has all the special bonds it needs.


-Justin

--
==

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

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

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

==

--
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[gmx-users] Problem fpr building a peptide with two modified residues with amber ff



--
Stéphane Abel, Ph.D.
Commissariat à l’Energie Atomique et aux Energies Alternatives
Centre de Saclay DSV/ISVFJ/SB2SM
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60

De : ABEL Stephane
Envoyé : dimanche 14 janvier 2018 16:52
À : gromacs.org_gmx-users@maillist.sys.kth.se
Objet : RE:gromacs.org_gmx-users Digest, Vol 165, Issue 50

Thanks Justin

First I forgot to say that I am building a cyclic peptide (Atosiban, 
https://fr.wikipedia.org/wiki/Atosiban). I construct two RTP for the  MER 
(3-Mercaptopropionyl-) and TYO (ethoxy tyrosine. And they are correct since the 
two residues are well constructed and linked together with pdb2gmx as it is 
shown If I consider the ILE as NILE

For linking the MER and CYX I define a bond with the specbond.dat (the 
corresponding bond is shown in the  pdb2gmx output). The only problem I have is 
that NILE residue is chosen instead of ILE

How to resolve this problem and to force pdb2gmx to use ILE ? It is strange or 
I found a subtle error I cannot find.

Stéphane




--

Message: 3
Date: Sun, 14 Jan 2018 10:34:08 -0500
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem fpr building a peptide with two
modified residues with amber ff
Message-ID: <541ddbd0-378e-16eb-79a4-f161235d4...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 1/14/18 10:04 AM, ABEL Stephane wrote:
> Hi Justin
>
> I have added the TYO and MER residue as Protein is the residuetypes.dat. And 
> the the following output with pdb2gmx. I select 2 and 6
>
> ##
>gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
> Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes
>
>
> Select the Force Field:
>  From '/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top/':
>   1: Amber12sb ff99SB + new backbone and side chain torsion for protein
>   2: AMBER14SB_parmbsc1 (ff14SB for protein + parmbsc1 for DNA)
>   3: AMBER94 BCL force field (J. Comp. Chem. 2012, 33, 1969?1980)
>   4: CHARMM36 all-atom force field (July 2017)
>   5: CHARMM36 all-atom force field, surfactants and pigments
>   6: GLYCAM06 force field for alkylglycosides and RG1 (2011, J. Phys. Chem. B 
> 2011, 115, 487-499 )
>   7: GROMOS96 2016H66 force field (J. Chem. Theory. Comput., 2016, 12, 
> 3825?3850)
>   8: GROMOS96 53a6 force field with PVP (JCC 2004 vol 25 pag 1656 and J. 
> Phys. Chem. C, 2015, 119 (14), pp 7888?7899)
>   9: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 
> 10.1002/jcc.21675)
> 10: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
> 10.1007/s00249-011-0700-9)
>  From '/ccc/products/gromacs-5.1.2/default/share/gromacs/top':
> 11: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
> 1999-2012, 2003)
> 12: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
> 13: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
> 461-469, 1996)
> 14: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
> 1049-1074, 2000)
> 15: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
> 2006)
> 16: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
> 78, 1950-58, 2010)
> 17: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
> 18: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
> 19: GROMOS96 43a1 force field
> 20: GROMOS96 43a2 force field (improved alkane dihedrals)
> 21: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> 22: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> 23: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 24: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
> 10.1007/s00249-011-0700-9)
> 25: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 2
>
> Using the Amber14sb_parmbsc1 force field in directory 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff
>
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/watermodels.dat
>
> Select the Water Model:
>   1: TIP3P TIP 3-point, recommended
>   2: TIP4P TIP 4-point
>   3: TIP4P-Ew  TIP 4-point optimized with Ewald
>   4: SPC   simple point charge
>   5: SPC/E extended simple point charge
>   6: None
> 6
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.r2b
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.r2b
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.r2b
> Reading Atosiban_box_ctr.pdb...
> Read 'GROningen MAchine for Chemical Simulation', 85 atoms
> Analyzing

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue 50

Thanks Justin 

First I forgot to say that I am building a cyclic peptide (Atosiban, 
https://fr.wikipedia.org/wiki/Atosiban). I construct two RTP for the  MER 
(3-Mercaptopropionyl-) and TYO (ethoxy tyrosine. And they are correct since the 
two residues are well constructed and linked together with pdb2gmx as it is 
shown If I consider the ILE as NILE 

For linking the MER and CYX I define a bond with the specbond.dat (the 
corresponding bond is shown in the  pdb2gmx output). The only problem I have is 
that NILE residue is chosen instead of ILE

How to resolve this problem and to force pdb2gmx to use ILE ? It is strange or 
I found a subtle error I cannot find.  

Stéphane 


 

--

Message: 3
Date: Sun, 14 Jan 2018 10:34:08 -0500
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem fpr building a peptide with two
modified residues with amber ff
Message-ID: <541ddbd0-378e-16eb-79a4-f161235d4...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 1/14/18 10:04 AM, ABEL Stephane wrote:
> Hi Justin
>
> I have added the TYO and MER residue as Protein is the residuetypes.dat. And 
> the the following output with pdb2gmx. I select 2 and 6
>
> ##
>gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
> Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes
>
>
> Select the Force Field:
>  From '/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top/':
>   1: Amber12sb ff99SB + new backbone and side chain torsion for protein
>   2: AMBER14SB_parmbsc1 (ff14SB for protein + parmbsc1 for DNA)
>   3: AMBER94 BCL force field (J. Comp. Chem. 2012, 33, 1969?1980)
>   4: CHARMM36 all-atom force field (July 2017)
>   5: CHARMM36 all-atom force field, surfactants and pigments
>   6: GLYCAM06 force field for alkylglycosides and RG1 (2011, J. Phys. Chem. B 
> 2011, 115, 487-499 )
>   7: GROMOS96 2016H66 force field (J. Chem. Theory. Comput., 2016, 12, 
> 3825?3850)
>   8: GROMOS96 53a6 force field with PVP (JCC 2004 vol 25 pag 1656 and J. 
> Phys. Chem. C, 2015, 119 (14), pp 7888?7899)
>   9: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 
> 10.1002/jcc.21675)
> 10: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
> 10.1007/s00249-011-0700-9)
>  From '/ccc/products/gromacs-5.1.2/default/share/gromacs/top':
> 11: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
> 1999-2012, 2003)
> 12: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
> 13: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
> 461-469, 1996)
> 14: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
> 1049-1074, 2000)
> 15: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
> 2006)
> 16: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
> 78, 1950-58, 2010)
> 17: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
> 18: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
> 19: GROMOS96 43a1 force field
> 20: GROMOS96 43a2 force field (improved alkane dihedrals)
> 21: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> 22: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> 23: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 24: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
> 10.1007/s00249-011-0700-9)
> 25: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 2
>
> Using the Amber14sb_parmbsc1 force field in directory 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff
>
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/watermodels.dat
>
> Select the Water Model:
>   1: TIP3P TIP 3-point, recommended
>   2: TIP4P TIP 4-point
>   3: TIP4P-Ew  TIP 4-point optimized with Ewald
>   4: SPC   simple point charge
>   5: SPC/E extended simple point charge
>   6: None
> 6
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.r2b
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.r2b
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.r2b
> Reading Atosiban_box_ctr.pdb...
> Read 'GROningen MAchine for Chemical Simulation', 85 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 0 blocks of water and 10 residues with 85 atoms
>
>chain  #res #atoms
>1 'A'10 85
>
> All occupancies are one
> Opening force field file 
> /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/atomtypes.atp
> Atomtype 89Reading residue database... (amber14sb_parmbsc1)
>
> Opening force field file 
>

Re: [gmx-users] rlist




On 1/14/18 10:42 AM, Faezeh Pousaneh wrote:

Thanks Justin. But I only define vdW potential form, coulomb potential form
is as in Gromacs. So I would like to have electrostatic interactions as
other systems, so are

   rlist = 0.9  (in nm)
   rcoulomb= 0.9  (in nm)

fine while I am using PME?


Again, there is no standard value here and it is dictated by the 
functional form being used. You have a custom interaction potential, 
even if you're using normal PME alongside you have user-defined, 
tabulated vdW interactions. Presumably there should be some evaluation 
of what cutoffs are used to satisfy whatever the assumptions are in the 
parametrization of your model, i.e. you need to have some target data of 
a known system that tells you that your physical model (cutoffs and 
functional form) is right, and then you use those same settings in 
whatever systems are of interest.


-Justin


Best regards


On Sun, Jan 14, 2018 at 3:46 PM, Justin Lemkul  wrote:



On 1/14/18 6:01 AM, Faezeh Pousaneh wrote:


Hi,

I have a system of charged hard spheres (user-potential), where the vdW
cut-off should be diameter of my molecule 0.3479. I wonder if I chose
rlist
and rcoulomb correctly? (see below please)


I'm not sure if anyone can tell you that. You're using custom potentials,
so setting cutoffs is part of the parametrization of that potential itself.

-Justin


integrator= md

   dt= 0.001
   nsteps= 3000
   nstxout   = 10   ; save coordinates every 0
ps
   nstvout   = 10   ; save velocities every 0
ps
   nstlog= 10   ; update log file every
   nstenergy = 10; save energies every
   nstxtcout = 10   ; Output frequency for xtc file
   xtc-precision = 10   ; precision for xtc file
   ns_type   = grid; search neighboring grid cells
   nstlist   = 10   ;  fs
   pbc   = xyz ; 3-D PBC
   rlist  = 0.9 ; short-range neighbor-list
cutoff (in nm)
   rcoulomb  = 0.9 ; short-range electrostatic
cutoff
(in nm)
   rvdw  = 0.3479  ; short-range van der Waals
cutoff
(in nm)
   coulombtype   = PME-user ; Particle Mesh Ewald for
long-range electrostatics
   pme_order = 4   ; cubic interpolation
   fourierspacing= 0.16; grid spacing for FFT
   vdw-type  = user
   Tcoupl= berendsen   ; modified Berendsen thermostat
   tc-grps   = co2   rest   ; two coupling groups -
more accurate
   tau_t =  0.1   0.1 ; time constant, in ps
   ref_t =  179.8  179.8 ; reference temperature, one
for
each group, in K
   ;tc-grps  = system
cutoff-scheme  =group
   energygrps= co2 rest
   Pcoupl=  berendsen ;Parrinello-Rahman
   Pcoupltype= Isotropic
   tau_p = 1.0
   compressibility   = 6.2e-5
   ref_p = 5500.0
   gen_vel   = yes
   gen_temp  = 179.8
   gen_seed  = 712349
   DispCorr  =no;  EnerPres; account for cut-off vdW
scheme
   constraints   = all-bonds   ; all bonds constrained (fixed
length)
   continuation  = no ; Restarting after NPT
   constraint-algorithm  =  lincs   ; holonomic constraints
   lincs_iter= 1   ; accuracy of LINCS
   lincs_order   = 4   ; also related to accuracy
Best regards


--
==

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

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

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

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==

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

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

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

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Re: [gmx-users] rlist

Thanks Justin. But I only define vdW potential form, coulomb potential form
is as in Gromacs. So I would like to have electrostatic interactions as
other systems, so are

  rlist = 0.9  (in nm)
  rcoulomb= 0.9  (in nm)

fine while I am using PME?

Best regards


On Sun, Jan 14, 2018 at 3:46 PM, Justin Lemkul  wrote:

>
>
> On 1/14/18 6:01 AM, Faezeh Pousaneh wrote:
>
>> Hi,
>>
>> I have a system of charged hard spheres (user-potential), where the vdW
>> cut-off should be diameter of my molecule 0.3479. I wonder if I chose
>> rlist
>> and rcoulomb correctly? (see below please)
>>
>
> I'm not sure if anyone can tell you that. You're using custom potentials,
> so setting cutoffs is part of the parametrization of that potential itself.
>
> -Justin
>
>
> integrator= md
>>   dt= 0.001
>>   nsteps= 3000
>>   nstxout   = 10   ; save coordinates every 0
>> ps
>>   nstvout   = 10   ; save velocities every 0
>> ps
>>   nstlog= 10   ; update log file every
>>   nstenergy = 10; save energies every
>>   nstxtcout = 10   ; Output frequency for xtc file
>>   xtc-precision = 10   ; precision for xtc file
>>   ns_type   = grid; search neighboring grid cells
>>   nstlist   = 10   ;  fs
>>   pbc   = xyz ; 3-D PBC
>>   rlist  = 0.9 ; short-range neighbor-list
>> cutoff (in nm)
>>   rcoulomb  = 0.9 ; short-range electrostatic
>> cutoff
>> (in nm)
>>   rvdw  = 0.3479  ; short-range van der Waals
>> cutoff
>> (in nm)
>>   coulombtype   = PME-user ; Particle Mesh Ewald for
>> long-range electrostatics
>>   pme_order = 4   ; cubic interpolation
>>   fourierspacing= 0.16; grid spacing for FFT
>>   vdw-type  = user
>>   Tcoupl= berendsen   ; modified Berendsen thermostat
>>   tc-grps   = co2   rest   ; two coupling groups -
>> more accurate
>>   tau_t =  0.1   0.1 ; time constant, in ps
>>   ref_t =  179.8  179.8 ; reference temperature, one
>> for
>> each group, in K
>>   ;tc-grps  = system
>> cutoff-scheme  =group
>>   energygrps= co2 rest
>>   Pcoupl=  berendsen ;Parrinello-Rahman
>>   Pcoupltype= Isotropic
>>   tau_p = 1.0
>>   compressibility   = 6.2e-5
>>   ref_p = 5500.0
>>   gen_vel   = yes
>>   gen_temp  = 179.8
>>   gen_seed  = 712349
>>   DispCorr  =no;  EnerPres; account for cut-off vdW
>> scheme
>>   constraints   = all-bonds   ; all bonds constrained (fixed
>> length)
>>   continuation  = no ; Restarting after NPT
>>   constraint-algorithm  =  lincs   ; holonomic constraints
>>   lincs_iter= 1   ; accuracy of LINCS
>>   lincs_order   = 4   ; also related to accuracy
>> Best regards
>>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
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Re: [gmx-users] energy group exclusion




On 1/14/18 9:59 AM, rose rahmani wrote:

Hello;

this is md_pull.mdp

integrator   = md
dt   = 0.002
nsteps   = 100
nstxout  = 5000
nstvout  = 5000
nstfout  = 500
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
nstlist  = 10
rlist= 1.5
cutoff-scheme= Verlet
energygrp-excl   = WAL WAL ZnS ZnS
coulombtype  = pme
rcoulomb = 1.2
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen_vel  = no
constraints  = h-bonds
ns_type  = grid
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrps   = SOL WAL ZnS Protein NA CL
energygrp-excl   = WAL WAL ZnS ZnS
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= ZnS
pull_group2_name= Protein
pull_coord1_type= umbrella
pull_coord1_geometry= direction
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_vec = 0 0 1
pull_coord1_rate= -0.001
pull_coord1_k   = 5000
pull_coord1_start   = yes
pull_nstxout= 10

--

ERROR 1 [file md_pull.mdp]:
   Energy group exclusions are not (yet) implemented for the Verlet scheme


WARNING 1 [file md_pull.mdp]:
   Can not exclude the lattice Coulomb energy between energy groups

Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.208 nm, buffer size 0.008 nm
Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 36x36x300, spacing 0.111 0.111 0.120
Pull group  natoms  pbc atom  distance at start  reference at t=0
1   560   280
226   773   1.763 nm  1.763 nm
Estimate for the relative computational load of the PME mesh part: 0.77

NOTE 3 [file md_pull.mdp]:
   The optimal PME mesh load for parallel simulations is below 0.5
   and for highly parallel simulations between 0.25 and 0.33,
   for higher performance, increase the cut-off and the PME grid spacing.


This run will generate roughly 149 Mb of data

There were 3 notes

There was 1 warning

There were 3 notes

There was 1 warning

---
Program gmx grompp, VERSION 5.1.4
Source code file:
/home/sjalili/gromacs-5.1.4/src/gromacs/gmxpreprocess/grompp.c, line: 2107

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

i implemented  energygr-excl in mdp file, so why get this error?!


Read the above - such exclusions are not compatible with either the 
Verlet scheme or with PME.



and my second question is that i want to pull Protein(to get closer to
sheet) to ZnS sheet, so should i use position restraint for Protein in this
step?


If you want to induce motion in some species, does it make sense to 
apply a biasing potential that prevents motion?



and what is the difference between geometry= direction or distance in my
system?


Please see the manual for a description of these features.

-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] Problem fpr building a peptide with two modified residues with amber ff




On 1/14/18 10:04 AM, ABEL Stephane wrote:

Hi Justin

I have added the TYO and MER residue as Protein is the residuetypes.dat. And 
the the following output with pdb2gmx. I select 2 and 6

##
   gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes


Select the Force Field:
 From '/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top/':
  1: Amber12sb ff99SB + new backbone and side chain torsion for protein
  2: AMBER14SB_parmbsc1 (ff14SB for protein + parmbsc1 for DNA)
  3: AMBER94 BCL force field (J. Comp. Chem. 2012, 33, 1969–1980)
  4: CHARMM36 all-atom force field (July 2017)
  5: CHARMM36 all-atom force field, surfactants and pigments
  6: GLYCAM06 force field for alkylglycosides and RG1 (2011, J. Phys. Chem. B 
2011, 115, 487-499 )
  7: GROMOS96 2016H66 force field (J. Chem. Theory. Comput., 2016, 12, 
3825−3850)
  8: GROMOS96 53a6 force field with PVP (JCC 2004 vol 25 pag 1656 and J. Phys. 
Chem. C, 2015, 119 (14), pp 7888–7899)
  9: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 
10.1002/jcc.21675)
10: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
 From '/ccc/products/gromacs-5.1.2/default/share/gromacs/top':
11: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
12: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
13: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
461-469, 1996)
14: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
1049-1074, 2000)
15: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
2006)
16: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
78, 1950-58, 2010)
17: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
18: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
19: GROMOS96 43a1 force field
20: GROMOS96 43a2 force field (improved alkane dihedrals)
21: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
22: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
23: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
24: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
25: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
2

Using the Amber14sb_parmbsc1 force field in directory 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff

Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/watermodels.dat

Select the Water Model:
  1: TIP3P TIP 3-point, recommended
  2: TIP4P TIP 4-point
  3: TIP4P-Ew  TIP 4-point optimized with Ewald
  4: SPC   simple point charge
  5: SPC/E extended simple point charge
  6: None
6
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.r2b
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.r2b
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.r2b
Reading Atosiban_box_ctr.pdb...
Read 'GROningen MAchine for Chemical Simulation', 85 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 10 residues with 85 atoms

   chain  #res #atoms
   1 'A'10 85

All occupancies are one
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/atomtypes.atp
Atomtype 89Reading residue database... (amber14sb_parmbsc1)

Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/Merca.rtp
Residue 1
Sorting it all out...
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/TYO.rtp
Residue 2
Sorting it all out...
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.rtp
Residue 95
Sorting it all out...
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.rtp
Residue 111
Sorting it all out...
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.rtp
Residue 127
Sorting it all out...
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.hdb
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.hdb
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.hdb
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.n.tdb

Re: [gmx-users] Problem fpr building a peptide with two modified residues with amber ff

Hi Justin

I have added the TYO and MER residue as Protein is the residuetypes.dat. And 
the the following output with pdb2gmx. I select 2 and 6

## 
  gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes


Select the Force Field:
From '/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top/':
 1: Amber12sb ff99SB + new backbone and side chain torsion for protein
 2: AMBER14SB_parmbsc1 (ff14SB for protein + parmbsc1 for DNA)
 3: AMBER94 BCL force field (J. Comp. Chem. 2012, 33, 1969–1980)
 4: CHARMM36 all-atom force field (July 2017)
 5: CHARMM36 all-atom force field, surfactants and pigments
 6: GLYCAM06 force field for alkylglycosides and RG1 (2011, J. Phys. Chem. B 
2011, 115, 487-499 )
 7: GROMOS96 2016H66 force field (J. Chem. Theory. Comput., 2016, 12, 3825−3850)
 8: GROMOS96 53a6 force field with PVP (JCC 2004 vol 25 pag 1656 and J. Phys. 
Chem. C, 2015, 119 (14), pp 7888–7899)
 9: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 
10.1002/jcc.21675)
10: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
From '/ccc/products/gromacs-5.1.2/default/share/gromacs/top':
11: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
12: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
13: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
461-469, 1996)
14: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
1049-1074, 2000)
15: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
2006)
16: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
78, 1950-58, 2010)
17: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
18: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
19: GROMOS96 43a1 force field
20: GROMOS96 43a2 force field (improved alkane dihedrals)
21: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
22: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
23: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
24: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
25: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
2

Using the Amber14sb_parmbsc1 force field in directory 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff

Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/watermodels.dat

Select the Water Model:
 1: TIP3P TIP 3-point, recommended
 2: TIP4P TIP 4-point
 3: TIP4P-Ew  TIP 4-point optimized with Ewald
 4: SPC   simple point charge
 5: SPC/E extended simple point charge
 6: None
6
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.r2b
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.r2b
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.r2b
Reading Atosiban_box_ctr.pdb...
Read 'GROningen MAchine for Chemical Simulation', 85 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 10 residues with 85 atoms

  chain  #res #atoms
  1 'A'10 85

All occupancies are one
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/atomtypes.atp
Atomtype 89Reading residue database... (amber14sb_parmbsc1)

Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/Merca.rtp
Residue 1
Sorting it all out...
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/TYO.rtp
Residue 2
Sorting it all out...
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.rtp
Residue 95
Sorting it all out...
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.rtp
Residue 111
Sorting it all out...
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.rtp
Residue 127
Sorting it all out...
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.hdb
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.hdb
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.hdb
Opening force field file 
/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.n.tdb
Opening force field file

[gmx-users] energy group exclusion

2018-01-14 Thread rose rahmani

Hello;

this is md_pull.mdp

integrator   = md
dt   = 0.002
nsteps   = 100
nstxout  = 5000
nstvout  = 5000
nstfout  = 500
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
nstlist  = 10
rlist= 1.5
cutoff-scheme= Verlet
energygrp-excl   = WAL WAL ZnS ZnS
coulombtype  = pme
rcoulomb = 1.2
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen_vel  = no
constraints  = h-bonds
ns_type  = grid
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrps   = SOL WAL ZnS Protein NA CL
energygrp-excl   = WAL WAL ZnS ZnS
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= ZnS
pull_group2_name= Protein
pull_coord1_type= umbrella
pull_coord1_geometry= direction
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_vec = 0 0 1
pull_coord1_rate= -0.001
pull_coord1_k   = 5000
pull_coord1_start   = yes
pull_nstxout= 10

--

ERROR 1 [file md_pull.mdp]:
  Energy group exclusions are not (yet) implemented for the Verlet scheme


WARNING 1 [file md_pull.mdp]:
  Can not exclude the lattice Coulomb energy between energy groups

Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.208 nm, buffer size 0.008 nm
Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 36x36x300, spacing 0.111 0.111 0.120
Pull group  natoms  pbc atom  distance at start  reference at t=0
   1   560   280
   226   773   1.763 nm  1.763 nm
Estimate for the relative computational load of the PME mesh part: 0.77

NOTE 3 [file md_pull.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing.


This run will generate roughly 149 Mb of data

There were 3 notes

There was 1 warning

There were 3 notes

There was 1 warning

---
Program gmx grompp, VERSION 5.1.4
Source code file:
/home/sjalili/gromacs-5.1.4/src/gromacs/gmxpreprocess/grompp.c, line: 2107

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

i implemented  energygr-excl in mdp file, so why get this error?!

and my second question is that i want to pull Protein(to get closer to
sheet) to ZnS sheet, so should i use position restraint for Protein in this
step?
and what is the difference between geometry= direction or distance in my
system?

Would you please help me?

With regards
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Re: [gmx-users] rlist




On 1/14/18 6:01 AM, Faezeh Pousaneh wrote:

Hi,

I have a system of charged hard spheres (user-potential), where the vdW
cut-off should be diameter of my molecule 0.3479. I wonder if I chose rlist
and rcoulomb correctly? (see below please)


I'm not sure if anyone can tell you that. You're using custom 
potentials, so setting cutoffs is part of the parametrization of that 
potential itself.


-Justin


integrator= md
  dt= 0.001
  nsteps= 3000
  nstxout   = 10   ; save coordinates every 0 ps
  nstvout   = 10   ; save velocities every 0 ps
  nstlog= 10   ; update log file every
  nstenergy = 10; save energies every
  nstxtcout = 10   ; Output frequency for xtc file
  xtc-precision = 10   ; precision for xtc file
  ns_type   = grid; search neighboring grid cells
  nstlist   = 10   ;  fs
  pbc   = xyz ; 3-D PBC
  rlist  = 0.9 ; short-range neighbor-list
cutoff (in nm)
  rcoulomb  = 0.9 ; short-range electrostatic cutoff
(in nm)
  rvdw  = 0.3479  ; short-range van der Waals cutoff
(in nm)
  coulombtype   = PME-user ; Particle Mesh Ewald for
long-range electrostatics
  pme_order = 4   ; cubic interpolation
  fourierspacing= 0.16; grid spacing for FFT
  vdw-type  = user
  Tcoupl= berendsen   ; modified Berendsen thermostat
  tc-grps   = co2   rest   ; two coupling groups -
more accurate
  tau_t =  0.1   0.1 ; time constant, in ps
  ref_t =  179.8  179.8 ; reference temperature, one for
each group, in K
  ;tc-grps  = system
cutoff-scheme  =group
  energygrps= co2 rest
  Pcoupl=  berendsen ;Parrinello-Rahman
  Pcoupltype= Isotropic
  tau_p = 1.0
  compressibility   = 6.2e-5
  ref_p = 5500.0
  gen_vel   = yes
  gen_temp  = 179.8
  gen_seed  = 712349
  DispCorr  =no;  EnerPres; account for cut-off vdW
scheme
  constraints   = all-bonds   ; all bonds constrained (fixed
length)
  continuation  = no ; Restarting after NPT
  constraint-algorithm  =  lincs   ; holonomic constraints
  lincs_iter= 1   ; accuracy of LINCS
  lincs_order   = 4   ; also related to accuracy
Best regards


--
==

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] Problem fpr building a peptide with two modified residues with amber ff

On 1/14/18 9:23 AM, ABEL Stephane wrote:

Dear all,

I have a peptide with two modified residues at the Nter with the following
sequence Mer-TYO-ILE-PHE.GLYNH2. Mer and TYO are a cap and a modified
tyrosine residue (side chain), respectively. the Mer, TYR and ILE are bonded
together with a peptide bond. To build the corresponding force field compatible
with Amber. I am using pdb2gmx with the following command (gmx5.1.2):

pdb2gmx -f mypeptide.pdb -p topol.top -o mypeptide.gro

the ILE residue are always recognized as the Nter residue of the peptide with NH3+ with the name NILE and thus I obtain
the "dangling bond" error Is it possible "to force" pdb2gmx to use a particular rtp entry (here
the central ILE residue) and consequently build the correct peptide bond between the TYO and ILE residues? Note that
the name of the isoleucine residue in " mypeptide.pdb" is "ILE" and not NILE.

I have also use pdb2gmx -f mypeptide.pdb -p topol.top -rtpres yes

but it does not work either

If Ile is being identified as the first residue, then you haven't added
your custom residues to residuetypes.dat as Protein.

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

Step 5 is what people always forget (and we've made a very prominent
warning message for the next release).

If that still doesn't work, please post the full screen output from
pdb2gmx; it is very verbose and makes it easy to spot the origin of the
problem.

-Justin

--
==

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

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

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

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[gmx-users] Problem fpr building a peptide with two modified residues with amber ff

Dear all, 

I have a peptide with two modified residues at the Nter with the following 
sequence Mer-TYO-ILE-PHE.GLYNH2. Mer and TYO are a cap and a modified 
tyrosine  residue (side chain), respectively. the Mer, TYR and ILE are bonded 
together with a peptide bond. To build the corresponding force field compatible 
with Amber. I am using pdb2gmx  with the following command (gmx5.1.2): 

pdb2gmx -f mypeptide.pdb  -p topol.top -o  mypeptide.gro

the ILE residue are always recognized as the Nter residue of the peptide with 
NH3+ with the name NILE and thus I obtain the "dangling bond" error  Is it 
possible "to force" pdb2gmx to use a particular rtp entry (here the central ILE 
residue) and consequently build the correct peptide bond between the TYO and 
ILE residues?  Note that the name of the isoleucine residue in " mypeptide.pdb" 
is "ILE" and not NILE.

I have also use pdb2gmx -f mypeptide.pdb  -p  topol.top  -rtpres yes 

but it does not work either

Thank for your help

Stéphane
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[gmx-users] selections

2018-01-14 Thread dgfd dgdfg

Greetings. Please help to solve simple task with gromacs selections.
Say, I have the box with 1000 identical molecules.
How to output the array of "nearest neigbours" (for example by distance between 
COM <5 Angstroms) for each molecule in the box at the time moment=T.


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[gmx-users] rlist