[gmx-users] Minimization and Equilibration in PMF

[Alex]

Dear gromacs user,

I was wondering if all the minimization and equlibrations(NVT and NPT)
which are necessary to be  done before every normal production run of MD,
should also be done in each windows of umbrella sampling in order to have a
good PMF curve? Or they can be waved and still have a good and reliable
curve.

Thanks,

Regards,
Alex
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[gmx-users] renaming DILE to ILE for Charmm27?

[Mijiddorj Batsaikhan]

Dear gmx users,

I want to make a simulation the peptide that contains D-ILE using Charmm
force field. Is it possible to rename the from DILE to ILE? and use pdb2gmx
to generate topology of the peptide.


Best regards,

Mijiddorj
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[gmx-users] D-amino acids' force field

[Mijiddorj Batsaikhan]

Dear users,

Hello, Is there any force field that contains parameters of D-amino acids?
In my case I need to D-ILE and D-Phe amino acids simulation. Please, advice
me.

Best regards,

Mijiddorj
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Re: [gmx-users] Switching Group to Verlet

[Mark Abraham]

Hi,

In theory, yes. But energy minimization is only sometimes done on a
cluster, and when it is done on one, it's mostly part of a larger workflow,
for which there is a lot more I/O, network and terminal-output traffic from
other GROMACS system-preparation tasks.

Mark

On Sat, Oct 22, 2016 at 2:48 PM Mahmood Naderan 
wrote:

> Well such message flooding  that is written in the log file at every step,
> the network will be a bottleneck affecting the performance of the other
> jobs
>
> Regards,
> Mahmood
>
>
>
> On Sat, Oct 22, 2016 at 3:42 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > This is an energy minimization. Its behaviour is to print every step, and
> > if that's verbose, it doesn't matter for the number of steps that are
> > typically required. A dynamical simulation has different needs and works
> > differently.
> >
> > Mark
> >
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Re: [gmx-users] Switching Group to Verlet

[Mahmood Naderan]

Well such message flooding  that is written in the log file at every step,
the network will be a bottleneck affecting the performance of the other jobs

Regards,
Mahmood



On Sat, Oct 22, 2016 at 3:42 PM, Mark Abraham 
wrote:

> Hi,
>
> This is an energy minimization. Its behaviour is to print every step, and
> if that's verbose, it doesn't matter for the number of steps that are
> typically required. A dynamical simulation has different needs and works
> differently.
>
> Mark
>
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 150, Issue 98

[Harimuthu]

Hello sir,
Sir you are tell to check dihedral angle of amino acid but for me the error
was in water molecules so how to overcome this please help me
With regards

On 22 Oct 2016 4:30 p.m., "Harimuthu"  wrote:

> Sir I have used opls forcefield and showing such a errors
> And this is the first time I am getting such a error
>
> On 22 Oct 2016 3:30 p.m.,  requ...@maillist.sys.kth.se> wrote:
>
>> Send gromacs.org_gmx-users mailing list submissions to
>> gromacs.org_gmx-users@maillist.sys.kth.se
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx
>> -users
>> or, via email, send a message with subject or body 'help' to
>> gromacs.org_gmx-users-requ...@maillist.sys.kth.se
>>
>> You can reach the person managing the list at
>> gromacs.org_gmx-users-ow...@maillist.sys.kth.se
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of gromacs.org_gmx-users digest..."
>>
>>
>> Today's Topics:
>>
>>1. Re: Switching Group to Verlet (Mahmood Naderan)
>>2. Re: Switching Group to Verlet (Mario Fern?ndez Pend?s)
>>3. Error in mdrun (Harimuthu)
>>4. D-amino acids' force fields (Mijiddorj Batsaikhan)
>>5. Re: D-amino acids' force fields (Tsjerk Wassenaar)
>>
>>
>> --
>>
>> Message: 1
>> Date: Fri, 21 Oct 2016 18:03:42 +0330
>> From: Mahmood Naderan 
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Switching Group to Verlet
>> Message-ID:
>> > gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> One more question.
>> Currently, gromacs prints the output on every step!
>>
>> Step=  159, Dmax= 3.8e-03 nm, Epot= -8.39592e+05 Fmax= 2.45536e+03, atom=
>> 2111
>> Step=  160, Dmax= 4.6e-03 nm, Epot= -8.39734e+05 Fmax= 4.30685e+03, atom=
>> 2111
>> Step=  161, Dmax= 5.5e-03 nm, Epot= -8.39913e+05 Fmax= 3.78613e+03, atom=
>> 2111
>>
>> Can you please tell me how to increase the print step? What is the
>> appropriate switch for that?
>>
>>
>> Regards,
>> Mahmood
>>
>>
>> --
>>
>> Message: 2
>> Date: Fri, 21 Oct 2016 15:46:25 +0100
>> From: Mario Fern?ndez Pend?s 
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Switching Group to Verlet
>> Message-ID:
>> > ail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Dear Mahmood,
>>
>> I always find very useful this page:
>> http://manual.gromacs.org/online/mdp_opt.html
>>
>> For your particular case I think you should look at
>> http://manual.gromacs.org/online/mdp_opt.html#out
>>
>> Cheers,
>> Mario
>>
>> 2016-10-21 15:33 GMT+01:00 Mahmood Naderan :
>> > One more question.
>> > Currently, gromacs prints the output on every step!
>> >
>> > Step=  159, Dmax= 3.8e-03 nm, Epot= -8.39592e+05 Fmax= 2.45536e+03,
>> atom=
>> > 2111
>> > Step=  160, Dmax= 4.6e-03 nm, Epot= -8.39734e+05 Fmax= 4.30685e+03,
>> atom=
>> > 2111
>> > Step=  161, Dmax= 5.5e-03 nm, Epot= -8.39913e+05 Fmax= 3.78613e+03,
>> atom=
>> > 2111
>> >
>> > Can you please tell me how to increase the print step? What is the
>> > appropriate switch for that?
>> >
>> >
>> > Regards,
>> > Mahmood
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>>
>> --
>>
>> Message: 3
>> Date: Fri, 21 Oct 2016 23:24:28 +0530
>> From: Harimuthu 
>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: [gmx-users] Error in mdrun
>> Message-ID:
>> > gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> hello sir
>>
>> While running the protein in water energy minimisation
>> gmx mdrun -v -deffnm em
>> an error is occurred as follows
>>
>> Program gmx mdrun, VERSION 5.1.2
>> Source code file:
>> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line:
>> 555
>>
>> Fatal error:
>>
>> step 14: Water molecule starting at atom 8686 can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate.
>>
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> in that i searched the error in input file which was in 8686 atom and
>> found
>> a error in coordinate value of water it was as
>> ATOM   8686  OW  SOL  1551   0.823  30.858  10.228  

Re: [gmx-users] nt/ntmpi/ntomp

[Mark Abraham]

Hi,

Please start with the documentation online...
http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html

Mark

On Sat, Oct 22, 2016 at 12:37 PM Mahmood Naderan 
wrote:

> Hi,
> What is the clear difference among nt, ntmpi and ntomp? I have built
> gromacs with MPI suppport. Then I run
>
> mpirun gmx_mpi mdrun
>
> Simply I want to know, is it a good idea to use 'nt' for such command? Are
> there some conflicts among them which degrade the performance? For example,
> using 'nt' for mpirun degrades the performance. Is that correct?
>
> How about ntomp?
> I read the descriptions for them, but I expect to see a table that shows
> which switch is valid/invalid for a platform.
>
>
>
> Regards,
> Mahmood
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Re: [gmx-users] Switching Group to Verlet

[Mark Abraham]

Hi,

This is an energy minimization. Its behaviour is to print every step, and
if that's verbose, it doesn't matter for the number of steps that are
typically required. A dynamical simulation has different needs and works
differently.

Mark

On Fri, Oct 21, 2016 at 4:34 PM Mahmood Naderan 
wrote:

> One more question.
> Currently, gromacs prints the output on every step!
>
> Step=  159, Dmax= 3.8e-03 nm, Epot= -8.39592e+05 Fmax= 2.45536e+03, atom=
> 2111
> Step=  160, Dmax= 4.6e-03 nm, Epot= -8.39734e+05 Fmax= 4.30685e+03, atom=
> 2111
> Step=  161, Dmax= 5.5e-03 nm, Epot= -8.39913e+05 Fmax= 3.78613e+03, atom=
> 2111
>
> Can you please tell me how to increase the print step? What is the
> appropriate switch for that?
>
>
> Regards,
> Mahmood
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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Re: [gmx-users] Negative average pressure value after NPT equilibration

[Mark Abraham]

Hi,

Negative pressure means the system wants to contract. But your simulations
are probably too short to get a reliable measurement of pressure, nor to
equilibrate it if you were not already very close to the right density. See
background at e.g. http://www.gromacs.org/Documentation/Terminology/Pressure
 and
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html


Mark

On Sat, Oct 22, 2016 at 1:34 PM Dario Akaberi  wrote:

> Dear users
>
> I am trying to perform the MD simulation of a protein in water using the
> amberFF99sb-ildn force field.
>
> To so so I created the protein topology specifying TIP3P water. then I
> created a dodecahedron box with -d 1.0, I filled it using spc216.gro. and
> added 7 NA ions. This resulted in a system of  8837 water molecules plus
> the 7 ions and the protein. Minimization were carried out using conjugate
> gradient method (gromacs is compiled with double precision) which converged
> to emtol 0.01 in 48000 steps.The following nvt ensemble worked well (I
> think) and the resulting average temperature was 299.702 (ref temperature
> was 300 K) with Err. Est. = 0.32  RMSD 4.39922 and tot-Drift 1.58106.
> Now the problems begin. After NVT equilibration I performed an NPT
> equilibration step of 100 ps which resulted in an average pressure of -50.
> I then tried to equilibrate for a longer time: 150 and 200 ps with the same
> result. I also tried a 500 ps NPT equilibration which resulted in an
> average  pressure of -60 and average density 998.935 with Err. Est = 0.12,
> RMSD = 2.38 and Tot-Drift = 0.83 /kg/m^3).
>
> This is the NPT.mdp file I used:
>
> define= -DPOSRES
> integrator   = md; leap-frog integrator
> nsteps   = 5 ; 2 * 5 = 100 ps
> dt  = 0.002; 2 fs
>
> nstxout   = 500; save coordinates every 1.0 ps
> nstvout   = 500; save velocities every 1.0 ps
> nstenergy   = 500; save energies every 1.0 ps
> nstlog = 500; update log file every 1.0 ps
>
> continuation= yes; Restarting after NVT
> constraint_algorithm= lincs; holonomic constraints
> constraints= all-bonds; all bonds (even heavy
> atom-H bonds) constrained
> lincs_iter= 1; accuracy of LINCS
> lincs_order= 4; also related to accuracy
>
> cutoff-scheme  = Verlet
> ns_type   = grid
> nstlist   = 10
> rlist   = 1.0
> rcoulomb= 1.0
> rvdw= 1.0
>
> coulombtype= PME
> pme_order= 4
> fourierspacing= 0.16
>
> ; Temperature coupling is on
> tcoupl= V-rescale; modified Berendsen
> thermostat
> tc-grps= Protein Non-Protein
> tau_t= 0.1  0.1
> ref_t= 300   300; reference
> temperature, one for each group, in K
>
> pcoupl= Parrinello-Rahman; Pressure
> coupling on in NPT
> pcoupltype= isotropic; uniform scaling
> of box vectors
> tau_p= 2.0; time constant, in ps
> ref_p= 1.0; reference pressure, in bar
> compressibility = 4.5e-5; isothermal
> compressibility of water, bar^-1
> refcoord_scaling= com  * I get an error
> without this
>
> ; Periodic boundary conditions
> pbc= xyz; 3-D PBC
> ; Dispersion correction
> DispCorr= EnerPres; account for cut-off
> vdW scheme
> ; Velocity generation
> gen_vel= no; Velocity generation is off
>
> I don't know what I'm doing wrong, and unfortunately, I am new to molecular
> dynamics simulation which doesn't help. I tried to find a solution and
> found some other cases where people had a negative pressure after NPT
> equilibration step but it was like an average pressure of -2 not -60!
> Any help would be very appreciated.
>
> Thanks,
>
> Dario
> --
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* For 

[gmx-users] Negative average pressure value after NPT equilibration

[Dario Akaberi]

Dear users

I am trying to perform the MD simulation of a protein in water using the
amberFF99sb-ildn force field.

To so so I created the protein topology specifying TIP3P water. then I
created a dodecahedron box with -d 1.0, I filled it using spc216.gro. and
added 7 NA ions. This resulted in a system of  8837 water molecules plus
the 7 ions and the protein. Minimization were carried out using conjugate
gradient method (gromacs is compiled with double precision) which converged
to emtol 0.01 in 48000 steps.The following nvt ensemble worked well (I
think) and the resulting average temperature was 299.702 (ref temperature
was 300 K) with Err. Est. = 0.32  RMSD 4.39922 and tot-Drift 1.58106.
Now the problems begin. After NVT equilibration I performed an NPT
equilibration step of 100 ps which resulted in an average pressure of -50.
I then tried to equilibrate for a longer time: 150 and 200 ps with the same
result. I also tried a 500 ps NPT equilibration which resulted in an
average  pressure of -60 and average density 998.935 with Err. Est = 0.12,
RMSD = 2.38 and Tot-Drift = 0.83 /kg/m^3).

This is the NPT.mdp file I used:

define= -DPOSRES
integrator   = md; leap-frog integrator
nsteps   = 5 ; 2 * 5 = 100 ps
dt  = 0.002; 2 fs

nstxout   = 500; save coordinates every 1.0 ps
nstvout   = 500; save velocities every 1.0 ps
nstenergy   = 500; save energies every 1.0 ps
nstlog = 500; update log file every 1.0 ps

continuation= yes; Restarting after NVT
constraint_algorithm= lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy
atom-H bonds) constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy

cutoff-scheme  = Verlet
ns_type   = grid
nstlist   = 10
rlist   = 1.0
rcoulomb= 1.0
rvdw= 1.0

coulombtype= PME
pme_order= 4
fourierspacing= 0.16

; Temperature coupling is on
tcoupl= V-rescale; modified Berendsen
thermostat
tc-grps= Protein Non-Protein
tau_t= 0.1  0.1
ref_t= 300   300; reference
temperature, one for each group, in K

pcoupl= Parrinello-Rahman; Pressure
coupling on in NPT
pcoupltype= isotropic; uniform scaling
of box vectors
tau_p= 2.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar
compressibility = 4.5e-5; isothermal
compressibility of water, bar^-1
refcoord_scaling= com  * I get an error
without this

; Periodic boundary conditions
pbc= xyz; 3-D PBC
; Dispersion correction
DispCorr= EnerPres; account for cut-off
vdW scheme
; Velocity generation
gen_vel= no; Velocity generation is off

I don't know what I'm doing wrong, and unfortunately, I am new to molecular
dynamics simulation which doesn't help. I tried to find a solution and
found some other cases where people had a negative pressure after NPT
equilibration step but it was like an average pressure of -2 not -60!
Any help would be very appreciated.

Thanks,

Dario
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 150, Issue 98

[Harimuthu]

Sir I have used opls forcefield and showing such a errors
And this is the first time I am getting such a error

On 22 Oct 2016 3:30 p.m., 
wrote:

> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se
>
> You can reach the person managing the list at
> gromacs.org_gmx-users-ow...@maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: Switching Group to Verlet (Mahmood Naderan)
>2. Re: Switching Group to Verlet (Mario Fern?ndez Pend?s)
>3. Error in mdrun (Harimuthu)
>4. D-amino acids' force fields (Mijiddorj Batsaikhan)
>5. Re: D-amino acids' force fields (Tsjerk Wassenaar)
>
>
> --
>
> Message: 1
> Date: Fri, 21 Oct 2016 18:03:42 +0330
> From: Mahmood Naderan 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Switching Group to Verlet
> Message-ID:
>  mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> One more question.
> Currently, gromacs prints the output on every step!
>
> Step=  159, Dmax= 3.8e-03 nm, Epot= -8.39592e+05 Fmax= 2.45536e+03, atom=
> 2111
> Step=  160, Dmax= 4.6e-03 nm, Epot= -8.39734e+05 Fmax= 4.30685e+03, atom=
> 2111
> Step=  161, Dmax= 5.5e-03 nm, Epot= -8.39913e+05 Fmax= 3.78613e+03, atom=
> 2111
>
> Can you please tell me how to increase the print step? What is the
> appropriate switch for that?
>
>
> Regards,
> Mahmood
>
>
> --
>
> Message: 2
> Date: Fri, 21 Oct 2016 15:46:25 +0100
> From: Mario Fern?ndez Pend?s 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Switching Group to Verlet
> Message-ID:
>  gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Mahmood,
>
> I always find very useful this page:
> http://manual.gromacs.org/online/mdp_opt.html
>
> For your particular case I think you should look at
> http://manual.gromacs.org/online/mdp_opt.html#out
>
> Cheers,
> Mario
>
> 2016-10-21 15:33 GMT+01:00 Mahmood Naderan :
> > One more question.
> > Currently, gromacs prints the output on every step!
> >
> > Step=  159, Dmax= 3.8e-03 nm, Epot= -8.39592e+05 Fmax= 2.45536e+03, atom=
> > 2111
> > Step=  160, Dmax= 4.6e-03 nm, Epot= -8.39734e+05 Fmax= 4.30685e+03, atom=
> > 2111
> > Step=  161, Dmax= 5.5e-03 nm, Epot= -8.39913e+05 Fmax= 3.78613e+03, atom=
> > 2111
> >
> > Can you please tell me how to increase the print step? What is the
> > appropriate switch for that?
> >
> >
> > Regards,
> > Mahmood
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> >
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> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
>
> --
>
> Message: 3
> Date: Fri, 21 Oct 2016 23:24:28 +0530
> From: Harimuthu 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Error in mdrun
> Message-ID:
>  mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> hello sir
>
> While running the protein in water energy minimisation
> gmx mdrun -v -deffnm em
> an error is occurred as follows
>
> Program gmx mdrun, VERSION 5.1.2
> Source code file:
> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line:
> 555
>
> Fatal error:
>
> step 14: Water molecule starting at atom 8686 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> in that i searched the error in input file which was in 8686 atom and found
> a error in coordinate value of water it was as
> ATOM   8686  OW  SOL  1551   0.823  30.858  10.228  1.00
> 0.00
> ATOM   8687  HW1 SOL  1551   0.825  31.173  11.177  1.00
> 0.00
> ATOM   8688  HW2 SOL  1551  95.631  30.777   9.906  1.00  0.00
>
> in this the third atom X coordinate is 95.631 and i changed it into 0.631 i
> dont know whether to relible or no, if i do potential graph it is good to
> see, so can anyone help me in solving this problem
> With regards
> 

[gmx-users] nt/ntmpi/ntomp

[Mahmood Naderan]

Hi,
What is the clear difference among nt, ntmpi and ntomp? I have built
gromacs with MPI suppport. Then I run

mpirun gmx_mpi mdrun

Simply I want to know, is it a good idea to use 'nt' for such command? Are
there some conflicts among them which degrade the performance? For example,
using 'nt' for mpirun degrades the performance. Is that correct?

How about ntomp?
I read the descriptions for them, but I expect to see a table that shows
which switch is valid/invalid for a platform.



Regards,
Mahmood
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[gmx-users] Bond distance and H bond

[Sameer Edirisinghe]

Dear users,

I need know how to find bond distance of H and O atoms of my polymer
molecule system which contain 10 molecules in a box. I used to modify .top
file .gro file to get 10 molecules in my system and i have successfully
perform the production run.

Then, I used following commands to find the bond distances to evaluate the
H bond formation.

1) gmx make_ndx

with above command, i need to know how to split 1 group into separate
groups as all of molecules has packed in same .gro file.


2) gmx distance

with above command im confusing how to select particular atom pair to find
distance at the prompt after running command.

Appreciate any guide here.
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Re: [gmx-users] D-amino acids' force fields

[Tsjerk Wassenaar]

Hi Mijidorj,

These amino acids are chemically and topologically equivalent to their L
counterparts. For united atom force fields you only need to invert the
improper dihedral at the C-alpha. For atomistic force fields you don't need
to change anything, except the CMAP stuff in Charmm for the backbone
dihedral, and you need to reset the hydrogen position if you used pdb2gmx
for building the topology and the hydrogens.

Cheers,

Tsjerk

On Oct 22, 2016 8:03 AM, "Mijiddorj Batsaikhan" 
wrote:

> Dear users,
>
> Hello, Is there any force field that contains parameters of D-amino acids?
> In my case I need to D-ILE and D-Phe amino acids simulation. Please, advice
> me.
>
> Best regards,
>
> Mijiddorj
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[gmx-users] D-amino acids' force fields

[Mijiddorj Batsaikhan]

Dear users,

Hello, Is there any force field that contains parameters of D-amino acids?
In my case I need to D-ILE and D-Phe amino acids simulation. Please, advice
me.

Best regards,

Mijiddorj
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