[gmx-users] Combination rules for VdW parameters with CHARMM36 forcefield

[Shrinath Kumar]

Hi all,

I'm trying to simulate a protein with the CHARMM36 forcefield. I'm using
PME for VdW interactions and since the CHARMM forcefield
uses Lorentz-Berthelot combining rules I set *lj-pme-comb-rule
= Lorentz-Berthelot *in my mdp file. When I try run grompp with the
following command

gmx grompp -f npt_umbrella.mdp -c ang5.gro -p ../topol.top -n ../groups.ndx
-o npt5.tpr -po nptOut.mdp

I get the following warning

"WARNING 1 [file npt_umbrella.mdp]:
  You are using arithmetic-geometric combination rules in LJ-PME, but your
  non-bonded C6 parameters do not follow these rules."

So I checked my topol.top file to ensure that I was using the correct
forcefield and indeed topol.top contains *#include
"./charmm36.ff/forcefield.itp". *Looking at forcefield.itp the [ default ]
section is as follows.

; This GROMACS version was created from:
; CHARMM parameters: multiple files
; CHARMM topology: multiple files
; Please see forcefield.doc for files and references
[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 1.0 1.0

>From sections 4.1.1 and 5.3.2 in the reference manual, comb-rule 2
corresponds to Lorentz-Berthelot rules. So I'm a bit confused by why the
warning is generated. I did also try with *lj-pme-comb-rule *set to
*Geometric*, but this again generated a note, instead of a warning this
time, that my non-bonded C6 parameters do not follow these rules.

Clearly, I'm missing something and I'd appreciate if someone could help me
figure out these warnings/notes.

I should also mention that I'm using Gromacs-2016-beta2 version (the latest
available on the cluster that I use) but I've also tried it on
gromacs-2016.4 on my local machine and got the same warnings.

Regards,
Shrinath
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Re: [gmx-users] hydration free energy

[dgfd dgdfg]

| Have you tried other FE estimate algorithms (i.e. thermodynamic
>integration, MBAR, etc.). Look into the project "alchemical-analysis". It's
>a python script that will give you some good visualizations on what is
>happening at that last step (it's compatible with GROMACS output files).
>There's an associated paper with it as well.
>
>Also double check that you are somehow not mistakingly leaving on some kind
>of interaction that is blowing up after everything else is decoupled 
Indeed it is mistake in my options. No TD method can produce good result with 
my data.
I wasn't careful. Now I see in dhdl.xvg for lambda=100 that :

@ s0 legend "dH/d\xl\f{} coul-lambda = 1."
@ s1 legend "dH/d\xl\f{} vdw-lambda = 1."
@ s2 legend "\xD\f{}H \xl\f{} to (1., 0.9800)"
@ s3 legend "\xD\f{}H \xl\f{} to (1., 1.)"
@ s4 legend "pV (kJ/mol)"
0. -30.652721 -425.07281 8.5014482 0.000 1.6549610
0.1000 -47.014614 -6562.4468 131.24881 0.000 1.6555369
0.2000 43.812706 -192491.17 3849.8198 0.000 1.6654193
...
...
...
1999.7000 115.17576 -4.0665294e+11 8.1330511e+09 0.000 1.5883621
1999.8000 -1642.2759 -5.8566267e+12 1.1713242e+11 0.000 1.5835983
1999.9000 3147.2195 -6.4759274e+11 1.2951842e+10 0.000 1.5708131
2000. 1253.8263 -5.8808771e+16 1.1761743e+15 0.000 1.5543262

dH/d vdw-lambda is tremendous which means that soft-core vdw must be used.

And one more question for specialists.
In pdf and online manuals I can't understand phrase about " sc-coul ":
"it is only taken into account when lambda states are used, not with  
couple-lambda0 /  couple-lambda1 "

But it is impossible to establist lambda-path (which is written in mdp-file as 
zero-based vector) without indication of it's initial and final states given by 
couple-lambda0/1.
And where is the equation describing  sc-coul similar to 4.136-4.138 about 
sc-vdw on page 98?
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Re: [gmx-users] hydration free energy

[Wes Barnett]

On Fri, Jan 5, 2018 at 2:29 PM,  wrote:

> Thanks for discussion. I am waiting already few days for anyfing reply.
> The technique of calculation in the file job.sh. The value of coul-λ is
> uniformely increasing from 0 to 1 with the step 0.02 for 50 first λ-steps
> and in the same way for vdw-λ last 50 λ-steps. The problem is in the last
> trajectory with λ=1 there are no coulomb and vdw intermolecular
> interactions with the estimate of the entropy according BAR method
> S=62204236256674537472.00 kT. The neigbouring state used in BAR with λ=0.99
> contains no coulomb and some remaining vdw force. Therefore I consider that
> overlapping of atoms can't produce this error. It happens only then
> opposite coulomb charges overcome vdw in nearly decoupled state. Therefore
> there is no need in soft-core interactions because all coulomb is decupling
> previously to vdw.
> I made the search in archive and this problem was discussed sometimes, but
> didn't found clear answer for my case. Now I decided to run the cycle in
> the reversed order from decoupled state to real interactions.
>
>
> ---
>
> You're welcome.
>
> If there are no vdW and Coul it still calculates the average energy, which
> without soft-core technique can be very large when atoms overlap.
> You can read
> http://www.sciencedirect.com/science/article/pii/S0010465516303411
>
> Eq. (2) and the following text etc.
>
> You can try a soft-core technique to see if it is better.
>
> Best,
> Asaf
> Quoting dgfd dgdfg :
>
> Hi,
>>
>>>
>>> Do you know which values of lambdas are used?
>>> Are you using a soft-core technique?
>>>
>>> Asaf
>>>
>> Thanks for discussion. I am waiting already few days for anyfing reply.
>> The technique of calculation in the file job.sh. The value of coul- λ is
>> uniformely increasing from 0 to 1 with the step 0.02 for 50 first  λ- steps
>> and in the same way for vdw- λ last 50  λ- steps. The problem is in the
>> last trajectory with  λ=1 there are no coulomb and vdw intermolecular
>> interactions with the estimate of the entropy according BAR method
>> S=62204236256674537472.00 kT. The neigbouring state used in BAR with
>> λ=0.99 contains no coulomb and some remaining vdw force. Therefore I
>> consider that overlapping of atoms can't produce this error. It happens
>> only then opposite coulomb charges overcome vdw in nearly decoupled state.
>> Therefore there is no need in soft-core interactions because all coulomb is
>> decupling previously to vdw.
>> I made the search in archive and this problem was discussed sometimes,
>> but didn't found clear answer for my case. Now I decided to run the cycle
>> in the reversed order from decoupled state to real interactions.
>>
>>
Have you tried other FE estimate algorithms (i.e. thermodynamic
integration, MBAR, etc.). Look into the project "alchemical-analysis". It's
a python script that will give you some good visualizations on what is
happening at that last step (it's compatible with GROMACS output files).
There's an associated paper with it as well.

Also double check that you are somehow not mistakingly leaving on some kind
of interaction that is blowing up after everything else is decoupled.

James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
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Re: [gmx-users] Minimization changes system box shape after using ParmEd

[Crystal Vander Zanden]

Thank you Dr. Lemkul,

I used trjconv as you suggested.  I also needed to add the -center flag.

gmx trjconv  -pbc mol -ur compact  -center -f em.gro -o em_trjconv.gro -s
em.tpr

Thank you for your help!
Crystal



> I am having problems maintaining the shape of my system box after using
> ParmEd to convert from Amber to Gromacs format.
>
> I parameterized a system with AmberTools (peptide solvated in an octahedral
> box).  I then converted the Amber files (.inpcrd and .prmtop) to GROMACS
> format (.gro and .top) using ParmEd.  I used VMD to look at the system, and
> it looks ok (peptide still centered in an octahedral box). (
> http://i1380.photobucket.com/albums/ah185/cmvander/parmed_zpssaq6ldnb.png)
>
> Next I did an energy minimization in GROMACS.  VMD displayed the resulting
> .gro file as a triclinic box and the peptide is no longer centered. (
> http://i1380.photobucket.com/albums/ah185/cmvander/
> minimized_zpsekznpl3w.png
> )
>
> I think that the system really is still an octahedral box because I can see
> the octahedral box boundaries within the triclinic box. I overlaid both
> systems and the protein is in the same spot (
> http://i1380.photobucket.com/albums/ah185/cmvander/image_
> overlay_zpsepfpqkvl.png).
> Also I got reasonable minimization energies.
>
> Steepest Descents converged to Fmax < 1000 in 337 steps
> Potential Energy  = -3.1393012e+05
> Maximum force =  9.0675385e+02 on atom 363
> Norm of force =  3.5674736e+01
>
> Am I just doing something wrong to cause VMD to display my system
> incorrectly, or is there a more serious issue?  Either way, I?d be happy to
> know how to fix it!
>
> Thanks in advance for any advice!  I really appreciate it!
> Crystal
>
>
> --
>
> GROMACS always uses a triclinic representation by default. Convert it to
> the desired shape with trjconv:
>
> gmx trjconv -pbc mol -ur compact
>
> -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] hydration free energy

[asaffarhi]

You can also read gromacs manual.
Best,
Asaf

Quoting asaffa...@post.tau.ac.il:

Am I need to use both sc-alpha and sc-coul in that case or it is  
enouth to write
sc-coul  = no   ; linear interpolation of  
Coulomb (none in this case)

as in the mentioned tutorial?


I don't have experience in the parameters. You can investigate it or  
wait for experienced people to respond.


Best,
Asaf


Quoting dgfd dgdfg :

If there are no vdW and Coul it still calculates the average  
energy, which without soft-core technique can be very large when  
atoms overlap.
You can read   
http://www.sciencedirect.com/science/article/pii/S0010465516303411  
Eq. (2) and the following text etc.

 >You can try a soft-core technique to see if it is better.
Am I need to use both sc-alpha and sc-coul in that case or it is  
enouth to write
sc-coul  = no   ; linear interpolation of  
Coulomb (none in this case)

as in the mentioned tutorial?

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Re: [gmx-users] hydration free energy

[asaffarhi]

Thanks for discussion. I am waiting already few days for anyfing reply.
The technique of calculation in the file job.sh. The value of coul-λ  
is uniformely increasing from 0 to 1 with the step 0.02 for 50 first  
λ-steps and in the same way for vdw-λ last 50 λ-steps. The problem is  
in the last trajectory with λ=1 there are no coulomb and vdw  
intermolecular interactions with the estimate of the entropy according  
BAR method S=62204236256674537472.00 kT. The neigbouring state used in  
BAR with λ=0.99 contains no coulomb and some remaining vdw force.  
Therefore I consider that overlapping of atoms can't produce this  
error. It happens only then opposite coulomb charges overcome vdw in  
nearly decoupled state. Therefore there is no need in soft-core  
interactions because all coulomb is decupling previously to vdw.
I made the search in archive and this problem was discussed sometimes,  
but didn't found clear answer for my case. Now I decided to run the  
cycle in the reversed order from decoupled state to real interactions.



---

You're welcome.

If there are no vdW and Coul it still calculates the average energy,  
which without soft-core technique can be very large when atoms overlap.

You can read
http://www.sciencedirect.com/science/article/pii/S0010465516303411

Eq. (2) and the following text etc.

You can try a soft-core technique to see if it is better.

Best,
Asaf
Quoting dgfd dgdfg :


Hi,


Do you know which values of lambdas are used?
Are you using a soft-core technique?

Asaf
Thanks for discussion. I am waiting already few days for anyfing  
reply. The technique of calculation in the file job.sh. The value of  
coul- λ is uniformely increasing from 0 to 1 with the step 0.02 for  
50 first  λ- steps and in the same way for vdw- λ last 50  λ- steps.  
The problem is in the last trajectory with  λ=1 there are no coulomb  
and vdw intermolecular interactions with the estimate of the entropy  
according BAR method S=62204236256674537472.00 kT. The neigbouring  
state used in BAR with  λ=0.99 contains no coulomb and  
some remaining vdw force. Therefore I consider that overlapping of  
atoms can't produce this error. It happens only then opposite  
coulomb charges overcome vdw in nearly decoupled state. Therefore  
there is no need in soft-core interactions because all coulomb is  
decupling previously to vdw.
I made the search in archive and this problem was discussed  
sometimes, but didn't found clear answer for my case. Now I decided  
to run the cycle in the reversed order from decoupled state to real  
interactions.


--


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Re: [gmx-users] hydration free energy

[asaffarhi]

Am I need to use both sc-alpha and sc-coul in that case or it is  
enouth to write
sc-coul  = no   ; linear interpolation of  
Coulomb (none in this case)

as in the mentioned tutorial?


I don't have experience in the parameters. You can investigate it or  
wait for experienced people to respond.


Best,
Asaf


Quoting dgfd dgdfg :

If there are no vdW and Coul it still calculates the average  
energy, which without soft-core technique can be very large when  
atoms overlap.
You can read   
http://www.sciencedirect.com/science/article/pii/S0010465516303411  
Eq. (2) and the following text etc.

 >You can try a soft-core technique to see if it is better.
Am I need to use both sc-alpha and sc-coul in that case or it is  
enouth to write
sc-coul  = no   ; linear interpolation of  
Coulomb (none in this case)

as in the mentioned tutorial?

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Re: [gmx-users] hydration free energy

[dgfd dgdfg]

>If there are no vdW and Coul it still calculates the average energy, which 
>without soft-core technique can be very large when atoms overlap.
>You can read  
>http://www.sciencedirect.com/science/article/pii/S0010465516303411 Eq. (2) and 
>the following text etc.
 >You can try a soft-core technique to see if it is better.
Am I need to use both sc-alpha and sc-coul in that case or it is enouth to write
sc-coul  = no   ; linear interpolation of Coulomb (none in 
this case)
as in the mentioned tutorial?

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Re: [gmx-users] hydration free energy

[dgfd dgdfg]

Hi,
>
>Do you know which values of lambdas are used?
>Are you using a soft-core technique?
>
>Asaf
Thanks for discussion. I am waiting already few days for anyfing reply. The 
technique of calculation in the file job.sh. The value of coul- λ is uniformely 
increasing from 0 to 1 with the step 0.02 for 50 first  λ- steps and in the 
same way for vdw- λ last 50  λ- steps. The problem is in the last trajectory 
with  λ=1 there are no coulomb and vdw intermolecular interactions with the 
estimate of the entropy according BAR method S=62204236256674537472.00 kT. The 
neigbouring state used in BAR with  λ=0.99 contains no coulomb and some 
remaining vdw force. Therefore I consider that overlapping of atoms can't 
produce this error. It happens only then opposite coulomb charges overcome vdw 
in nearly decoupled state. Therefore there is no need in soft-core interactions 
because all coulomb is decupling previously to vdw.
I made the search in archive and this problem was discussed sometimes, but 
didn't found clear answer for my case. Now I decided to run the cycle in the 
reversed order from decoupled state to real interactions.

--


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Re: [gmx-users] REMD implicit solvent

[Urszula Uciechowska]

Hi,

I should run it by using mdrun_mpi?

best
Urszula

> Hello,
>
>  From my experience, the domain decomposition is not compatible with
> implicit solvent, you have to switch
> to particle decomposition for the simulations.
>
>
> All the best,
> Qinghua
>
> On 01/05/2018 12:40 PM, Urszula Uciechowska wrote:
>> Hi,
>>
>> I just run a normal single-replica. Now the error that I have is:
>>
>> Program mdrun_mpi, VERSION 4.5.5
>> Source code file: domdec.c, line: 3266
>>
>> Software inconsistency error:
>> Inconsistent DD boundary staggering limits!
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> Any suggestions? What can I do to run it?
>>
>> Thanks
>> Ula
>>
>>> Hi,
>>>
>>> Did you try to debug your setup by running a normal single-replica
>>> simulation first?
>>>
>>> Mark
>>>
>>> On Fri, Jan 5, 2018 at 12:12 PM Urszula Uciechowska <
>>> urszula.uciechow...@biotech.ug.edu.pl> wrote:
>>>

 Dear gromacs users,

 I am trying to run REMD simulations using 4.5.5 version (implicit
 solvent). The MD procedure:

 pdb2gmx -f  prot.pdb -o prot.gro -q prot.pdb -ignh -ss.

 The input for minimization step:

 ; Run control parameters
 integrator   = cg
 nsteps   = 800
 vdwtype  = cut-off
 coulombtype  = cut-off
 ;cutoff-scheme= group
 pbc  = no
 periodic_molecules   = no
 nstlist  = 10
 ns_type  = grid
 rlist= 1.0
 rcoulomb = 1.6
 rvdw = 1.6
 comm-mode= Angular
 nstcomm  = 10
 ;
 ;Energy minimizing stuff
 ;
 emtol= 100.0
 nstcgsteep   = 2
 emstep   = 0.01
 ;
 ;Relative dielectric constant for the medium and the reaction field
 epsilon_r= 1
 epsilon_rf   = 1
 ;
 ; Implicit solvent
 ;
 implicit_solvent = GBSA
 gb_algorithm = OBC  ;Still  HCT   OBC
 nstgbradii   = 1.0
 rgbradii = 1.0  ; [nm] Cut-off for the calculation
 of
 the Born radii. Currently must be equal to rlist
 gb_epsilon_solvent   = 80   ; Dielectric constant for the
 implicit
 solvent
 gb_saltconc  = 0; Salt concentration for implicit
 solvent models, currently not used
 sa_algorithm = Ace-approximation
 sa_surface_tension   = 2.05016  ; Surface tension (kJ/mol/nm^2)
 for
 the SA (nonpolar surface) part of GBSA. The value -1 will set default
 value for Still/HCT/OBC GB-models.

 and it finished without errors.

 The problem is with equilibration step. The input file that I used is:

 ; MD CONTROL OPTIONS
 integrator  = md
 dt  = 0.002
 nsteps  = 5 ; 10 ns
 init_step   = 0; For exact run continuation or
 redoing part of a run
 comm-mode   = Angular  ; mode for center of mass
 motion
 removal
 nstcomm = 10   ; number of steps for center of
 mass motion removal

 ; OUTPUT CONTROL OPTIONS
 ; Output frequency for coords (x), velocities (v) and forces (f)
 nstxout  = 1000
 nstvout  = 1000
 nstfout  = 1000

 ; Output frequency for energies to log file and energy file
 nstlog   = 1000
 nstcalcenergy= 10
 nstenergy= 1000

 ; Neighbor searching and Electrostatitcs
 vdwtype  = cut-off
 coulombtype  = cut-off
 ;cutoff-scheme= group
 pbc  = no
 periodic_molecules   = no
 nstlist  = 5
 ns_type  = grid
 rlist= 1.0
 rcoulomb = 1.6
 rvdw = 1.0
 ; Selection of energy groups
 energygrps   = fixed not_fixed
 freezegrps   = fixed not_fixed
 freezedim= Y Y Y N N N

 ;Relative dielectric constant for the medium and the reaction field
 epsilon_r= 1
 epsilon_rf   = 1

 ; Temperutare coupling
 tcoupl   = v-rescale
 tc_grps  = fixed not_fixed
 tau_t= 0.01 0.01
 ;nst_couple   = 5
 ref_t= 300.00 300.00

 ; Pressure coupling
 pcoupl   = no
 ;pcoupletype  = isotropic
 tau_p= 1.0
 ;compressiblity   = 4.5e-5
 ref_p= 1.0
 gen_vel  = yes
 gen_temp = 

Re: [gmx-users] Catenation error

[Qinghua Liao]

Hello,

I guess that the difference might come from different number of waters, 
you can first strip all waters from the trajectory files,

and then combine them all into one single trajectory file.


All the best,
Qinghua

On 01/05/2018 01:04 PM, suniba wrote:

Hello experts and users

I have performed 4 simulations of same system starting with different initial 
conformations. Now when I am trying to catenate the trajectories with gmc 
trjcat, It is showing error that can’t catenate multiple trajectories with 
different number of atoms. I am not sure why the atom number is different since 
the system is same in all cases.
With Regards
Suniba


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[gmx-users] Catenation error

[suniba]

Hello experts and users

I have performed 4 simulations of same system starting with different initial 
conformations. Now when I am trying to catenate the trajectories with gmc 
trjcat, It is showing error that can’t catenate multiple trajectories with 
different number of atoms. I am not sure why the atom number is different since 
the system is same in all cases. 
With Regards
Suniba
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Re: [gmx-users] REMD implicit solvent

[Qinghua Liao]

Hello,

From my experience, the domain decomposition is not compatible with 
implicit solvent, you have to switch

to particle decomposition for the simulations.


All the best,
Qinghua

On 01/05/2018 12:40 PM, Urszula Uciechowska wrote:

Hi,

I just run a normal single-replica. Now the error that I have is:

Program mdrun_mpi, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Any suggestions? What can I do to run it?

Thanks
Ula


Hi,

Did you try to debug your setup by running a normal single-replica
simulation first?

Mark

On Fri, Jan 5, 2018 at 12:12 PM Urszula Uciechowska <
urszula.uciechow...@biotech.ug.edu.pl> wrote:



Dear gromacs users,

I am trying to run REMD simulations using 4.5.5 version (implicit
solvent). The MD procedure:

pdb2gmx -f  prot.pdb -o prot.gro -q prot.pdb -ignh -ss.

The input for minimization step:

; Run control parameters
integrator   = cg
nsteps   = 800
vdwtype  = cut-off
coulombtype  = cut-off
;cutoff-scheme= group
pbc  = no
periodic_molecules   = no
nstlist  = 10
ns_type  = grid
rlist= 1.0
rcoulomb = 1.6
rvdw = 1.6
comm-mode= Angular
nstcomm  = 10
;
;Energy minimizing stuff
;
emtol= 100.0
nstcgsteep   = 2
emstep   = 0.01
;
;Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
;
; Implicit solvent
;
implicit_solvent = GBSA
gb_algorithm = OBC  ;Still  HCT   OBC
nstgbradii   = 1.0
rgbradii = 1.0  ; [nm] Cut-off for the calculation
of
the Born radii. Currently must be equal to rlist
gb_epsilon_solvent   = 80   ; Dielectric constant for the
implicit
solvent
gb_saltconc  = 0; Salt concentration for implicit
solvent models, currently not used
sa_algorithm = Ace-approximation
sa_surface_tension   = 2.05016  ; Surface tension (kJ/mol/nm^2) for
the SA (nonpolar surface) part of GBSA. The value -1 will set default
value for Still/HCT/OBC GB-models.

and it finished without errors.

The problem is with equilibration step. The input file that I used is:

; MD CONTROL OPTIONS
integrator  = md
dt  = 0.002
nsteps  = 5 ; 10 ns
init_step   = 0; For exact run continuation or
redoing part of a run
comm-mode   = Angular  ; mode for center of mass motion
removal
nstcomm = 10   ; number of steps for center of
mass motion removal

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 1000
nstvout  = 1000
nstfout  = 1000

; Output frequency for energies to log file and energy file
nstlog   = 1000
nstcalcenergy= 10
nstenergy= 1000

; Neighbor searching and Electrostatitcs
vdwtype  = cut-off
coulombtype  = cut-off
;cutoff-scheme= group
pbc  = no
periodic_molecules   = no
nstlist  = 5
ns_type  = grid
rlist= 1.0
rcoulomb = 1.6
rvdw = 1.0
; Selection of energy groups
energygrps   = fixed not_fixed
freezegrps   = fixed not_fixed
freezedim= Y Y Y N N N

;Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1

; Temperutare coupling
tcoupl   = v-rescale
tc_grps  = fixed not_fixed
tau_t= 0.01 0.01
;nst_couple   = 5
ref_t= 300.00 300.00

; Pressure coupling
pcoupl   = no
;pcoupletype  = isotropic
tau_p= 1.0
;compressiblity   = 4.5e-5
ref_p= 1.0
gen_vel  = yes
gen_temp = 300.00 300.00
gen_seed = -1
constraints  = h-bonds


; Implicit solvent
implicit_solvent = GBSA
gb_algorithm = Still ; HCT  ; OBC
nstgbradii   = 1.0
rgbradii = 1.0  ; [nm] Cut-off for the
calculation
of the Born radii. Currently must be equal to rlist
gb_epsilon_solvent   = 80   ; Dielectric constant for the
implicit solvent
gb_saltconc  = 0; Salt concentration for
implicit
solvent models, currently not used
sa_algorithm = Ace-approximation
sa_surface_tension   = 2.05016  ; Surface tension (kJ/mol/nm^2)
for the SA (nonpolar surface) part of GBSA. The value -1 will set
default

Re: [gmx-users] REMD implicit solvent

[Urszula Uciechowska]

Hi,

I just run a normal single-replica. Now the error that I have is:

Program mdrun_mpi, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Any suggestions? What can I do to run it?

Thanks
Ula

> Hi,
>
> Did you try to debug your setup by running a normal single-replica
> simulation first?
>
> Mark
>
> On Fri, Jan 5, 2018 at 12:12 PM Urszula Uciechowska <
> urszula.uciechow...@biotech.ug.edu.pl> wrote:
>
>>
>>
>> Dear gromacs users,
>>
>> I am trying to run REMD simulations using 4.5.5 version (implicit
>> solvent). The MD procedure:
>>
>> pdb2gmx -f  prot.pdb -o prot.gro -q prot.pdb -ignh -ss.
>>
>> The input for minimization step:
>>
>> ; Run control parameters
>> integrator   = cg
>> nsteps   = 800
>> vdwtype  = cut-off
>> coulombtype  = cut-off
>> ;cutoff-scheme= group
>> pbc  = no
>> periodic_molecules   = no
>> nstlist  = 10
>> ns_type  = grid
>> rlist= 1.0
>> rcoulomb = 1.6
>> rvdw = 1.6
>> comm-mode= Angular
>> nstcomm  = 10
>> ;
>> ;Energy minimizing stuff
>> ;
>> emtol= 100.0
>> nstcgsteep   = 2
>> emstep   = 0.01
>> ;
>> ;Relative dielectric constant for the medium and the reaction field
>> epsilon_r= 1
>> epsilon_rf   = 1
>> ;
>> ; Implicit solvent
>> ;
>> implicit_solvent = GBSA
>> gb_algorithm = OBC  ;Still  HCT   OBC
>> nstgbradii   = 1.0
>> rgbradii = 1.0  ; [nm] Cut-off for the calculation
>> of
>> the Born radii. Currently must be equal to rlist
>> gb_epsilon_solvent   = 80   ; Dielectric constant for the
>> implicit
>> solvent
>> gb_saltconc  = 0; Salt concentration for implicit
>> solvent models, currently not used
>> sa_algorithm = Ace-approximation
>> sa_surface_tension   = 2.05016  ; Surface tension (kJ/mol/nm^2) for
>> the SA (nonpolar surface) part of GBSA. The value -1 will set default
>> value for Still/HCT/OBC GB-models.
>>
>> and it finished without errors.
>>
>> The problem is with equilibration step. The input file that I used is:
>>
>> ; MD CONTROL OPTIONS
>> integrator  = md
>> dt  = 0.002
>> nsteps  = 5 ; 10 ns
>> init_step   = 0; For exact run continuation or
>> redoing part of a run
>> comm-mode   = Angular  ; mode for center of mass motion
>> removal
>> nstcomm = 10   ; number of steps for center of
>> mass motion removal
>>
>> ; OUTPUT CONTROL OPTIONS
>> ; Output frequency for coords (x), velocities (v) and forces (f)
>> nstxout  = 1000
>> nstvout  = 1000
>> nstfout  = 1000
>>
>> ; Output frequency for energies to log file and energy file
>> nstlog   = 1000
>> nstcalcenergy= 10
>> nstenergy= 1000
>>
>> ; Neighbor searching and Electrostatitcs
>> vdwtype  = cut-off
>> coulombtype  = cut-off
>> ;cutoff-scheme= group
>> pbc  = no
>> periodic_molecules   = no
>> nstlist  = 5
>> ns_type  = grid
>> rlist= 1.0
>> rcoulomb = 1.6
>> rvdw = 1.0
>> ; Selection of energy groups
>> energygrps   = fixed not_fixed
>> freezegrps   = fixed not_fixed
>> freezedim= Y Y Y N N N
>>
>> ;Relative dielectric constant for the medium and the reaction field
>> epsilon_r= 1
>> epsilon_rf   = 1
>>
>> ; Temperutare coupling
>> tcoupl   = v-rescale
>> tc_grps  = fixed not_fixed
>> tau_t= 0.01 0.01
>> ;nst_couple   = 5
>> ref_t= 300.00 300.00
>>
>> ; Pressure coupling
>> pcoupl   = no
>> ;pcoupletype  = isotropic
>> tau_p= 1.0
>> ;compressiblity   = 4.5e-5
>> ref_p= 1.0
>> gen_vel  = yes
>> gen_temp = 300.00 300.00
>> gen_seed = -1
>> constraints  = h-bonds
>>
>>
>> ; Implicit solvent
>> implicit_solvent = GBSA
>> gb_algorithm = Still ; HCT  ; OBC
>> nstgbradii   = 1.0
>> rgbradii = 1.0  ; [nm] Cut-off for the
>> calculation
>> of the Born radii. Currently must be equal to rlist
>> gb_epsilon_solvent   = 80   ; Dielectric constant for the
>> implicit solvent
>> gb_saltconc  = 0; Salt concentration for
>> implicit
>> solvent models, currently not used
>> sa_algorithm = 

Re: [gmx-users] REMD implicit solvent

[Mark Abraham]

Hi,

Did you try to debug your setup by running a normal single-replica
simulation first?

Mark

On Fri, Jan 5, 2018 at 12:12 PM Urszula Uciechowska <
urszula.uciechow...@biotech.ug.edu.pl> wrote:

>
>
> Dear gromacs users,
>
> I am trying to run REMD simulations using 4.5.5 version (implicit
> solvent). The MD procedure:
>
> pdb2gmx -f  prot.pdb -o prot.gro -q prot.pdb -ignh -ss.
>
> The input for minimization step:
>
> ; Run control parameters
> integrator   = cg
> nsteps   = 800
> vdwtype  = cut-off
> coulombtype  = cut-off
> ;cutoff-scheme= group
> pbc  = no
> periodic_molecules   = no
> nstlist  = 10
> ns_type  = grid
> rlist= 1.0
> rcoulomb = 1.6
> rvdw = 1.6
> comm-mode= Angular
> nstcomm  = 10
> ;
> ;Energy minimizing stuff
> ;
> emtol= 100.0
> nstcgsteep   = 2
> emstep   = 0.01
> ;
> ;Relative dielectric constant for the medium and the reaction field
> epsilon_r= 1
> epsilon_rf   = 1
> ;
> ; Implicit solvent
> ;
> implicit_solvent = GBSA
> gb_algorithm = OBC  ;Still  HCT   OBC
> nstgbradii   = 1.0
> rgbradii = 1.0  ; [nm] Cut-off for the calculation of
> the Born radii. Currently must be equal to rlist
> gb_epsilon_solvent   = 80   ; Dielectric constant for the implicit
> solvent
> gb_saltconc  = 0; Salt concentration for implicit
> solvent models, currently not used
> sa_algorithm = Ace-approximation
> sa_surface_tension   = 2.05016  ; Surface tension (kJ/mol/nm^2) for
> the SA (nonpolar surface) part of GBSA. The value -1 will set default
> value for Still/HCT/OBC GB-models.
>
> and it finished without errors.
>
> The problem is with equilibration step. The input file that I used is:
>
> ; MD CONTROL OPTIONS
> integrator  = md
> dt  = 0.002
> nsteps  = 5 ; 10 ns
> init_step   = 0; For exact run continuation or
> redoing part of a run
> comm-mode   = Angular  ; mode for center of mass motion
> removal
> nstcomm = 10   ; number of steps for center of
> mass motion removal
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout  = 1000
> nstvout  = 1000
> nstfout  = 1000
>
> ; Output frequency for energies to log file and energy file
> nstlog   = 1000
> nstcalcenergy= 10
> nstenergy= 1000
>
> ; Neighbor searching and Electrostatitcs
> vdwtype  = cut-off
> coulombtype  = cut-off
> ;cutoff-scheme= group
> pbc  = no
> periodic_molecules   = no
> nstlist  = 5
> ns_type  = grid
> rlist= 1.0
> rcoulomb = 1.6
> rvdw = 1.0
> ; Selection of energy groups
> energygrps   = fixed not_fixed
> freezegrps   = fixed not_fixed
> freezedim= Y Y Y N N N
>
> ;Relative dielectric constant for the medium and the reaction field
> epsilon_r= 1
> epsilon_rf   = 1
>
> ; Temperutare coupling
> tcoupl   = v-rescale
> tc_grps  = fixed not_fixed
> tau_t= 0.01 0.01
> ;nst_couple   = 5
> ref_t= 300.00 300.00
>
> ; Pressure coupling
> pcoupl   = no
> ;pcoupletype  = isotropic
> tau_p= 1.0
> ;compressiblity   = 4.5e-5
> ref_p= 1.0
> gen_vel  = yes
> gen_temp = 300.00 300.00
> gen_seed = -1
> constraints  = h-bonds
>
>
> ; Implicit solvent
> implicit_solvent = GBSA
> gb_algorithm = Still ; HCT  ; OBC
> nstgbradii   = 1.0
> rgbradii = 1.0  ; [nm] Cut-off for the calculation
> of the Born radii. Currently must be equal to rlist
> gb_epsilon_solvent   = 80   ; Dielectric constant for the
> implicit solvent
> gb_saltconc  = 0; Salt concentration for implicit
> solvent models, currently not used
> sa_algorithm = Ace-approximation
> sa_surface_tension   = 2.05016  ; Surface tension (kJ/mol/nm^2)
> for the SA (nonpolar surface) part of GBSA. The value -1 will set default
> value for Still/HCT/OBC GB-models.
>
>
> mdrun -v -multidir eq_[12345678]
>
> The error that I obtained is:
>
> Fatal error:
> A charge group moved too far between two domain decomposition steps
> This usually means that your system is not well equilibrated
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> I do 

[gmx-users] REMD implicit solvent

[Urszula Uciechowska]

Dear gromacs users,

I am trying to run REMD simulations using 4.5.5 version (implicit
solvent). The MD procedure:

pdb2gmx -f  prot.pdb -o prot.gro -q prot.pdb -ignh -ss.

The input for minimization step:

; Run control parameters
integrator   = cg
nsteps   = 800
vdwtype  = cut-off
coulombtype  = cut-off
;cutoff-scheme= group
pbc  = no
periodic_molecules   = no
nstlist  = 10
ns_type  = grid
rlist= 1.0
rcoulomb = 1.6
rvdw = 1.6
comm-mode= Angular
nstcomm  = 10
;
;Energy minimizing stuff
;
emtol= 100.0
nstcgsteep   = 2
emstep   = 0.01
;
;Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
;
; Implicit solvent
;
implicit_solvent = GBSA
gb_algorithm = OBC  ;Still  HCT   OBC
nstgbradii   = 1.0
rgbradii = 1.0  ; [nm] Cut-off for the calculation of
the Born radii. Currently must be equal to rlist
gb_epsilon_solvent   = 80   ; Dielectric constant for the implicit
solvent
gb_saltconc  = 0; Salt concentration for implicit
solvent models, currently not used
sa_algorithm = Ace-approximation
sa_surface_tension   = 2.05016  ; Surface tension (kJ/mol/nm^2) for
the SA (nonpolar surface) part of GBSA. The value -1 will set default
value for Still/HCT/OBC GB-models.

and it finished without errors.

The problem is with equilibration step. The input file that I used is:

; MD CONTROL OPTIONS
integrator  = md
dt  = 0.002
nsteps  = 5 ; 10 ns
init_step   = 0; For exact run continuation or
redoing part of a run
comm-mode   = Angular  ; mode for center of mass motion
removal
nstcomm = 10   ; number of steps for center of
mass motion removal

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 1000
nstvout  = 1000
nstfout  = 1000

; Output frequency for energies to log file and energy file
nstlog   = 1000
nstcalcenergy= 10
nstenergy= 1000

; Neighbor searching and Electrostatitcs
vdwtype  = cut-off
coulombtype  = cut-off
;cutoff-scheme= group
pbc  = no
periodic_molecules   = no
nstlist  = 5
ns_type  = grid
rlist= 1.0
rcoulomb = 1.6
rvdw = 1.0
; Selection of energy groups
energygrps   = fixed not_fixed
freezegrps   = fixed not_fixed
freezedim= Y Y Y N N N

;Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1

; Temperutare coupling
tcoupl   = v-rescale
tc_grps  = fixed not_fixed
tau_t= 0.01 0.01
;nst_couple   = 5
ref_t= 300.00 300.00

; Pressure coupling
pcoupl   = no
;pcoupletype  = isotropic
tau_p= 1.0
;compressiblity   = 4.5e-5
ref_p= 1.0
gen_vel  = yes
gen_temp = 300.00 300.00
gen_seed = -1
constraints  = h-bonds


; Implicit solvent
implicit_solvent = GBSA
gb_algorithm = Still ; HCT  ; OBC
nstgbradii   = 1.0
rgbradii = 1.0  ; [nm] Cut-off for the calculation
of the Born radii. Currently must be equal to rlist
gb_epsilon_solvent   = 80   ; Dielectric constant for the
implicit solvent
gb_saltconc  = 0; Salt concentration for implicit
solvent models, currently not used
sa_algorithm = Ace-approximation
sa_surface_tension   = 2.05016  ; Surface tension (kJ/mol/nm^2)
for the SA (nonpolar surface) part of GBSA. The value -1 will set default
value for Still/HCT/OBC GB-models.


mdrun -v -multidir eq_[12345678]

The error that I obtained is:

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I do not know what is wrong. I checked the Fatal error at
www.gromacs.org/Documentation/Errors. My system is ok, I tried to increase
the min steps but did not help. I have also checked the
http://www.gromacs.org/Documentation/How-tos/REMD but can not move forward
because of equilibration step.

I appreciate any recommendation.

Thanks

Urszula



Urszula Uciechowska PhD
University of Gdansk and Medical Univesity of Gdansk

Re: [gmx-users] KALP in DPPC

[Piggot T .]

If you are wanting to study things under physiological conditions I'd ask why 
are you looking at DPPC?

Generally speaking physiological membranes are in the liquid crystal phase 
(although this is a vast simplification of the heterogeneous and specialised 
natures of different membranes) and this is one of the reasons why people would 
typically use 323 K for DPPC. If you wish to use 310 K I would chose another 
lipid (e.g. POPC).

Cheers

Tom

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of 
kordza...@aut.ac.ir [kordza...@aut.ac.ir]
Sent: 05 January 2018 04:56
To: gromacs org gmx-users
Subject: [gmx-users] KALP in DPPC

Hi Dr.Lemkul

Thank you very much for your answer

I will select 310 kelvin becauase I want to investigate physiological condition.

in tutorial weve used semiisotropic pressure coupling and normal and 
lateral pressure are determined 1 bar.

why? is it related to surface tension?

if we want to surface tension be zero, should we set lateral pressure zero?

Thank you very much for your help

Regards

Azadeh

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Re: [gmx-users] hydration free energy

[asaffarhi]

Hi,

Do you know which values of lambdas are used?
Are you using a soft-core technique?

Asaf

Quoting dgfd dgdfg :

Hi. I have calculated deltaG of hydration for my molecule in 101  
steps. First 50 steps I decoupled coulomb interactions and last 50 -  
vdw. After all I calculated resulting value by the command

gmx bar -f {0..100}/dhdl.xvg -o -oi -oh -b 500 >RESULT
and found such phrase in the output

Temperature: 300 K
Detailed results in kT (see help for explanation):
 lam_A  lam_B  DG   +/- s_A   +/- s_B   +/-   stdev   +/-
 0  1    8.16  0.11    0.34  0.06    0.34  0.06    0.91  0.02
 1  2    7.61  0.07    0.21  0.08    0.19  0.07    0.86  0.01
...
...
...
    97 98   -0.40  0.02    0.42  0.02    0.55  0.02    0.97  0.01
    98 99   -2.11  0.03    1.16  0.03    1.84  0.06    1.75  0.03
    99    100  -17.55  0.43   13.60  0.44 62204236256674537472.00  
33302891096617504768.00  102.60 10.21

WARNING: Some of these results violate the Second Law of Thermodynamics:
 This is can be the result of severe undersampling, or (more likely)
 there is something wrong with the simulations.

Please answer what is wrong in my simple algorythm. It is based on  
tutorial   
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html with some simplification. All necessary data  
attached.


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