[gmx-users] gmx mindist

[‪Mohammad Roostaie‬ ‪]

Hi,
Which distance does the gmx mindist command compute? Is it the minimum distance 
between the center of mass of the first group due to the other group?
Thanks,Mohammad
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Re: [gmx-users] NPT problem

[‪Mohammad Roostaie‬ ‪]

The graphene is 9*9 nm, and I proposed the box to be 11*11 nm. Do you mean that 
the box dimensions are small and thats the problem?
Thanks,Mohammad
  From: Alex 
 To: Discussion list for GROMACS users ; Discussion list 
for GROMACS users  
 Sent: Friday, 14 July 2017, 11:31:06
 Subject: Re: [gmx-users] NPT problem
   

>
> I used "gmx x2top -f gr.gro -o topol1.top -ff cnt_oplsaa -name CNT 
> -noparam -pbc" for generating the topology. then I used "gmx editconf 
> -f grvmdn.pdb -o gr.gro -box 11 11 11 -angles 90 90 90" for creating 
> the box
>
And where did "-box 11 11 11" come from? For pbc to work the box in your 
case has to be a certain size corresponding to the graphene dimensions. 
And no, it is not simply its approximate X-Y dimensions.

Alex

>
> 
> *From:* Alex 
> *To:* Discussion list for GROMACS users ; 
> Mohammad Roostaie 
> *Sent:* Thursday, 13 July 2017, 22:51:48
> *Subject:* Re: [gmx-users] NPT problem
>
> Also, that tutorial's parameters that are completely wrong for 
> graphene. For bulk graphene bond types I suggest:
>
> CJ    CJ      1    0.14200  420420.0
>
> For bulk angles:
>
> CJ    CJ    CJ      1  120.000    659.346
>
> For bulk dihedrals:
>
>  CJ    CJ    CJ    CJ      3 17.30770  0.0 -17.30770  
> 0.0 0.0  0.0
>
> These are parameters obtained from a Taylor-expanded optimized 
> Tersoff-Brenner potential. Please count the number of bonds and 
> dihedrals in your graphene model, as produced by x2top. If the number 
> of dihedrals divided by the number of bonds gives you a number, say, 
> equal to m, then multiply the dihedral parameters by that number. And 
> do NOT use bond constraints -- you are simulating a crystal.
>
> Alex
>
> On Thu, Jul 13, 2017 at 10:45 AM,  > wrote:
>
>    Hi All GROMACS users,
>
>
>
>    I created graphene with nanotube modeler then I created a force
>    field for graphene based on OPLS (by using this link and its
>    parameters: http://chembytes.wikidot.com/ grocnt
>    ). I generated the topology
>    file using x2top command. I put the graphene inside a box of water
>    (TIP3P) which was larger than the graphene dimension with 1000
>      (kJ/mol nm^2) position restraint on all the atoms, and I
>    performed the energy minimization and NVT equilibrations (in order
>    to get an optimized structure of the graphene for further
>    simulations). The results of both of them were good (energy level
>    has reached a negative value with the order of 6 and the
>    temperature has converged the preferred value). But, when I run
>    the NPT equilibration, the results are not good (the pressure and
>    density fluctuated very much and the averaged values are so far
>    from the preferred ones). Also, during the NPT run, I received
>    these messages:
>
>
>    step 53965: Water molecule starting at atom 127424 can not be settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote pdb files with previous and current coordinates
>
>
>
>    step 141454: Water molecule starting at atom 53366 can not be settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote pdb files with previous and current coordinates
>
>
>
>    step 141483: Water molecule starting at atom 53366 can not be settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote pdb files with previous and current coordinates
>
>
>
>    step 323815: Water molecule starting at atom 30509 can not be settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote pdb files with previous and current coordinates
>
>
>
>    step 323816: Water molecule starting at atom 30509 can not be settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote pdb files with previous and current coordinates
>
>
>
>    step 323818: Water molecule starting at atom 30509 can not be settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote pdb files with previous and current coordinates
>
>
>
>    step 355712: Water molecule starting at atom 121748 can not be
>    settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote pdb files with previous and current coordinates
>
>
>
>    step 355714: Water molecule starting at atom 121748 can not be
>    settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote pdb files with previous and current coordinates
>
>
>
>    step 355716: Water molecule starting at atom 121748 can not be
>    settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote 

Re: [gmx-users] NPT problem

[‪Mohammad Roostaie‬ ‪]

Hi Alex, Thank you for your reply.
By the term "results were good or not" I meant that whether the temperature, 
pressure, and density have converged to the preferred values or not (I 
mentioned it in the parenthesis, too).
I used "gmx x2top -f gr.gro -o topol1.top -ff cnt_oplsaa -name CNT -noparam 
-pbc" for generating the topology. then I used "gmx editconf -f grvmdn.pdb -o 
gr.gro -box 11 11 11 -angles 90 90 90" for creating the box then I filled it 
with water with "gmx solvate -cp gr.gro -cs spc216.gro -o gr_solv.gro -p 
topol.top" command. The x2top does not require the box dimensions. Should I use 
the "-pbc" option in editconf, too? Do you mean that first I should perform EM, 
NVT, NPT, and MD run on the graphene alone without water and any position 
restraints? Also, I followed the tutorial step by step. Also, I used it since 
this tutorial is mentioned on Gromacs website. Actually, I think that in this 
tutorial, the purpose is to generate a force filed for graphene based on OPLS 
force field. Moreover, I added the ffbonded.itp, ffnonbonded.itp, and tip3p.itp 
files from OPLS-AA force field to the directory for the water molecules. Also, 
after optimization of the graphene, I want to put a peptide inside the box, so 
I should add those files, also I think that I should add the aminoacids.rtp for 
the peptide in order to use a unique force field for all the molecules and not 
to use different force fields.
Kind regards,Mohammad



  From: Alex 
 To: Discussion list for GROMACS users ; Mohammad 
Roostaie  
 Sent: Thursday, 13 July 2017, 22:51:48
 Subject: Re: [gmx-users] NPT problem
   
Also, that tutorial's parameters that are completely wrong for graphene. For 
bulk graphene bond types I suggest:
  CJ    CJ      1    0.14200   420420.0 

For bulk angles:
  CJ     CJ     CJ      1   120.000    659.346  

For bulk dihedrals:
  CJ     CJ     CJ     CJ      3     17.30770   0.0 -17.30770   0.0   
0.0   0.0
These are parameters obtained from a Taylor-expanded optimized Tersoff-Brenner 
potential. Please count the number of bonds and dihedrals in your graphene 
model, as produced by x2top. If the number of dihedrals divided by the number 
of bonds gives you a number, say, equal to m, then multiply the dihedral 
parameters by that number. And do NOT use bond constraints -- you are 
simulating a crystal.
Alex
On Thu, Jul 13, 2017 at 10:45 AM,  wrote:

Hi All GROMACS users,


 
I created graphene with nanotube modeler then I created a force field for 
graphene based on OPLS (by using this link and its parameters: 
http://chembytes.wikidot.com/ grocnt). I generated the topology file using 
x2top command. I put the graphene inside a box of water (TIP3P) which was 
larger than the graphene dimension with 1000  (kJ/mol nm^2) position restraint 
on all the atoms, and I performed the energy minimization and NVT 
equilibrations (in order to get an optimized structure of the graphene for 
further simulations). The results of both of them were good (energy level has 
reached a negative value with the order of 6 and the temperature has converged 
the preferred value). But, when I run the NPT equilibration, the results are 
not good (the pressure and density fluctuated very much and the averaged values 
are so far from the preferred ones). Also, during the NPT run, I received these 
messages:


step 53965: Water molecule starting at atom 127424 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 141454: Water molecule starting at atom 53366 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 141483: Water molecule starting at atom 53366 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323815: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323816: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323818: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355712: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355714: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files 

[gmx-users] NPT problem

[‪Mohammad Roostaie‬ ‪]

Hi All GROMACS users,


 
I created graphene with nanotube modeler then I created a force field for 
graphene based on OPLS (by using this link and its parameters: 
http://chembytes.wikidot.com/grocnt). I generated the topology file using x2top 
command. I put the graphene inside a box of water (TIP3P) which was larger than 
the graphene dimension with 1000  (kJ/mol nm^2) position restraint on all the 
atoms, and I performed the energy minimization and NVT equilibrations (in order 
to get an optimized structure of the graphene for further simulations). The 
results of both of them were good (energy level has reached a negative value 
with the order of 6 and the temperature has converged the preferred value). 
But, when I run the NPT equilibration, the results are not good (the pressure 
and density fluctuated very much and the averaged values are so far from the 
preferred ones). Also, during the NPT run, I received these messages:


step 53965: Water molecule starting at atom 127424 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 141454: Water molecule starting at atom 53366 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 141483: Water molecule starting at atom 53366 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323815: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323816: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323818: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355712: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355714: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355716: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355718: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 469414: Water molecule starting at atom 101579 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 469416: Water molecule starting at atom 101579 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 469418: Water molecule starting at atom 101579 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 469420: Water molecule starting at atom 101579 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
, and a pdb file was saved after each step.
In addition, something interesting is that I performed another run with all of 
the previous parameters, except I did not put position restraint on the 
graphene, and the results of NPT were good and acceptable, and I did not get 
those messages.


Can you please help me figure this problem out? Since I should put the position 
restrain on the graphene. I really would appreciate any help.


If you need further information please let me know.
Kind regards,Mohammad
 

 
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Re: [gmx-users] Modifying force field for graphene

[‪Mohammad Roostaie‬ ‪]

Thank you very much Alex.
Mohammad

  From: Alex <nedoma...@gmail.com>
 To: gmx-us...@gromacs.org; ‪Mohammad Roostaie‬ ‪ <mohammad.r0...@yahoo.com> 
 Sent: Tuesday, 11 July 2017, 22:54:56
 Subject: Re: [gmx-users] Modifying force field for graphene
   
The answer is yes, OPLSAA does need to be slightly edited for graphene 
and nanotubes to work, assuming you find good parameters for graphene. 
Google is strong with you, use it.

Alex

On 7/11/2017 8:34 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Hi All,
> I want to simulate graphene by using OPLS_AA force field. Does this force 
> field need any modification for graphene simulation?If yes, do you have any 
> link tutorial for the modification?
> Kind regards,Mohammad



   
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[gmx-users] Modifying force field for graphene

[‪Mohammad Roostaie‬ ‪]

Hi All,
I want to simulate graphene by using OPLS_AA force field. Does this force field 
need any modification for graphene simulation?If yes, do you have any link 
tutorial for the modification?
Kind regards,Mohammad
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Re: [gmx-users] Nano-structures equilibration

[‪Mohammad Roostaie‬ ‪]

Thank you very much, Alex. I also performed the process on GPU, and I got the 
below error:
step 1: Water molecule starting at atom 96743 can not be settled.Check for bad 
contacts and/or reduce the timestep if appropriate.Wrote pdb files with 
previous and current coordinates
WARNING: Listed nonbonded interaction between particles 4321 and 4328at 
distance 21.231 which is larger than the table limit 1.853 nm.
This is likely either a 1,4 interaction, or a listed interaction insidea 
smaller molecule you are decoupling during a free energy calculation.Since 
interactions at distances beyond the table cannot be computed,they are skipped 
until they are inside the table limit again. You willonly see this message 
once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there isprobably 
something wrong with your system. Only change the table-extensiondistance in 
the mdp file if you are really sure that is the reason.
I would appreciate any help.
Regards,Mohammad

  From: Alex 
 To: gmx-us...@gromacs.org 
 Sent: Friday, 30 June 2017, 22:21:26
 Subject: Re: [gmx-users] Nano-structures equilibration
  
You have performance-related errors, maybe try a different number of 
ranks, or another machine, or OpenMP instead of MPI -- hope others will 
be able to comment on technical issues.
Your question was whether you should abandon nanostructure equilibration 
because of this -- the answer is of course no.

Alex


On 6/30/2017 5:03 AM, Mohammad Roostaie wrote:
> I asked it since I got some errors regarding the NPT equilibration, 
> also this link says that turn off the pressure coupling.
>
> The errors which I received is as follow:
>
> Fatal error:
> The number of ranks you selected (14) contains a large prime factor 7. 
> In most cases this will lead to bad performance. Choose a number with 
> smaller prime factors or set the decomposition (option -dd) manually.
> For more information and tips for troubleshooting, please check the 
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> —---—
>
> Halting parallel program mdrun_mpi on rank 0 out of 14
> —
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
>
> Furthermore, I used -dd (with the values of 7 2 1) option, and I got 
> this error:
>
> Fatal error:
> 1130 particles communicated to PME rank 14 are more than 2/3 times the 
> cut-off out of the domain decomposition cell of their charge group in 
> dimension y.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the 
> GROMACS
> website at Errors - Gromacs
>
> Regards,
> M
>
> 
> On Friday, June 30, 2017, 12:47:05 PM GMT+4:30, Alex 
>  wrote:
>
>
> Is this a philosophical question? Yes, it is certainly possible for
> graphene+peptide to exist in water under pressure.
>
>
> On 6/30/2017 12:05 AM, Mohammad Roostaie wrote:
> > Hi All,
> > Is it possible and necessary to run NPT equilibration process on the 
> nanostructure systems (graphene+peptide in water)? Since I got some 
> errors regarding this process.
> > Regards,Mohammad
> >
>

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[gmx-users] NPT error

[‪Mohammad Roostaie‬ ‪]

Hi All,


 
I wanted to perform NPT equilibration, but I got this error:


 
Fatal error:The number of ranks you selected (14) contains a large prime factor 
7. In most cases this will lead to bad performance. Choose a number with 
smaller prime factors or set the decomposition (option -dd) manually.For more 
information and tips for troubleshooting, please check the GROMACSwebsite at 
http://www.gromacs.org/Documentation/Errors—---—
Halting parallel program mdrun_mpi on rank 0 out of 
14—MPI_ABORT
 was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.You may or 
may not see output from other processes, depending on
exactly when Open MPI kills them. 



I performed energy minimization and NVT successfully, and the final energy 
level was 30864982016.00 kJ/mol

Can you please help me figure this out? If you need further information please 
let me know.


Regards,Mohammad
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Re: [gmx-users] mdp options in GROMACS 4.5.5

[‪Mohammad Roostaie‬ ‪]

Dear Mark,
I was using version 5.1.4, but I got this error when using "gmx mdrun":
tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted

I tried version 5.0.4, too, and I got the same error. Hence, I decided to use 
the 4.5.5 version which does not give me that error.
Mohammad

  From: Mark Abraham 
 To: gmx-us...@gromacs.org; mohammad.r0...@yahoo.com 
 Sent: Wednesday, 7 June 2017, 13:02:46
 Subject: Re: [gmx-users] mdp options in GROMACS 4.5.5
   
Hi,You almost certainly don't want to use version 4.5.5. It's many years old, 
slow and contains many bugs that have been fixed. Get a new version installed 
;-)Mark
On Tue, 6 Jun 2017 17:49 João Henriques  wrote:

Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I
mean, not the integration).

/J

On Tue, Jun 6, 2017 at 5:45 PM, João Henriques  wrote:

> Hi!
>
> I'm not sure Verlet was already implemented in GMX 4.5.5, but check the
> manual for that version (or the closest one).
>
> Cheers,
>
> /J
>
> On Tue, Jun 6, 2017 at 3:27 PM,  wrote:
>
>> Hi All,
>> I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp -
>> used as input into grompp to generate em.tpr
>> integrator      = steep         ; Algorithm (steep = steepest descent
>> minimization)
>> emtol           = 1000.0        ; Stop minimization when the maximum
>> force < 1000.0 kJ/mol/nm
>> emstep      = 0.01      ; Energy step size
>> nsteps          = 5         ; Maximum number of (minimization) steps
>> to perform
>>
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> nstlist             = 1             ; Frequency to update the neighbor
>> list and long range forces
>> cutoff-scheme   = Verlet
>> ns_type             = grid              ; Method to determine neighbor
>> list (simple, grid)
>> coulombtype         = PME               ; Treatment of long range
>> electrostatic interactions
>> rcoulomb            = 1.0               ; Short-range electrostatic
>> cut-off
>> rvdw                = 1.0               ; Short-range Van der Waals
>> cut-off
>> pbc                     = xyz           ; Periodic Boundary Conditions
>> (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error
>> which said that the cutoff-scheme is not recognized. what should I write
>> instead of "cutoff-scheme" in this version?
>> Thanks,Mohammad
>> --
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>>
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>> /Mailing_Lists/GMX-Users_List before posting!
>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>
>
>
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[gmx-users] Fw: mdp options in GROMACS 4.5.5

[‪Mohammad Roostaie‬ ‪]

Hi João,
Thank you very much. I removed this line from the mdp file.
Regards,Mohammad

  From: João Henriques 
 To: gmx-us...@gromacs.org; mohammad.r0...@yahoo.com 
 Sent: Tuesday, 6 June 2017, 20:18:51
 Subject: Re: [gmx-users] mdp options in GROMACS 4.5.5
  
Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I mean, 
not the integration).
/J
On Tue, Jun 6, 2017 at 5:45 PM, João Henriques  
wrote:

Hi!
I'm not sure Verlet was already implemented in GMX 4.5.5, but check the manual 
for that version (or the closest one).
Cheers,
/J
On Tue, Jun 6, 2017 at 3:27 PM,  wrote:

Hi All,
I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - used as 
input into grompp to generate em.tpr
integrator      = steep         ; Algorithm (steep = steepest descent 
minimization)
emtol           = 1000.0        ; Stop minimization when the maximum force < 
1000.0 kJ/mol/nm
emstep      = 0.01      ; Energy step size
nsteps          = 5         ; Maximum number of (minimization) steps to 
perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist             = 1             ; Frequency to update the neighbor list and 
long range forces
cutoff-scheme   = Verlet
ns_type             = grid              ; Method to determine neighbor list 
(simple, grid)
coulombtype         = PME               ; Treatment of long range electrostatic 
interactions
rcoulomb            = 1.0               ; Short-range electrostatic cut-off
rvdw                = 1.0               ; Short-range Van der Waals cut-off
pbc                     = xyz           ; Periodic Boundary Conditions 
(yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error 
which said that the cutoff-scheme is not recognized. what should I write 
instead of "cutoff-scheme" in this version?
Thanks,Mohammad
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[gmx-users] mdp options in GROMACS 4.5.5

[‪Mohammad Roostaie‬ ‪]

Hi All,
I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - used as 
input into grompp to generate em.tpr
integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 
1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to 
perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and 
long range forces
cutoff-scheme   = Verlet
ns_type = grid  ; Method to determine neighbor list 
(simple, grid)
coulombtype = PME   ; Treatment of long range electrostatic 
interactions
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions 
(yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error 
which said that the cutoff-scheme is not recognized. what should I write 
instead of "cutoff-scheme" in this version?
Thanks,Mohammad
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[gmx-users] tMPI error

[‪Mohammad Roostaie‬ ‪]

Hi All,



I wanted to run energy minimization process by this command: gmx mdrun -v 
-deffnm em. But, I got this error:
tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted
I do not know what the problem exactly is. Can you please help me?
Thanks,Mohammad

   
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Re: [gmx-users] EM error

[‪Mohammad Roostaie‬ ‪]

Can anyone please help me?
Mohammad

  From: ‪Mohammad Roostaie‬ ‪ <mohammad.r0...@yahoo.com>
 To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> 
 Sent: Wednesday, 31 May 2017, 8:27:59
 Subject: EM error
   
Hi All,
I wanted to run energy minimization process by this command: gmx mdrun -v 
-deffnm em. But, I got this error:
tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted
I do not know what the problem exactly is. Can you please help me?
Thanks,Mohammad

   
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[gmx-users] EM error

[‪Mohammad Roostaie‬ ‪]

Hi All,
I wanted to run energy minimization process by this command: gmx mdrun -v 
-deffnm em. But, I got this error:
tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted
I do not know what the problem exactly is. Can you please help me?
Thanks,Mohammad

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Re: [gmx-users] Genion error

[‪Mohammad Roostaie‬ ‪]

Thank you very much Justin. It is good now.
Best,Mohammad

  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org 
 Sent: Monday, 29 May 2017, 23:40:06
 Subject: Re: [gmx-users] Genion error
   


On 5/29/17 4:35 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Thank you Justin. Here is the link to access the topology 
> file:https://www.dropbox.com/sh/x58tzpmg0vzkbtg/AADH_efF_s8jKx4OaHN8a7IPa?dl=0
> 
> By the way, I do not know about your advice. Can you please give me the link?

It's somewhere in the archive.  Run the topology through dos2unix and always 
make sure to use a plain text editor.  See if that works.

-Justin

> Kind regards,Mohammad
> 
>        From: Justin Lemkul <jalem...@vt.edu>
>  To: gmx-us...@gromacs.org
>  Sent: Monday, 29 May 2017, 0:21:10
>  Subject: Re: [gmx-users] Genion error
>    
> 
> 
> On 5/28/17 3:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:
>> Hi All, when I wanted to add ions to the system, I got this error:
>> Fatal error:No line with moleculetype 'SOL' found the [ molecules ] section 
>> of file 'gr.top'For more information and tips for troubleshooting, please 
>> check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
>> However, there is 'SOL' molecule type in the [ molecules ] section of the 
>> topology file. Can you please help me to solve this problem?
> 
> Upload your topology to a file-sharing service and provide the URL to access 
> it.
>    There's no way to know what's going on (and I recall giving some previous
> advice about line endings - have you checked this?)
> 
> -Justin
> 

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Genion error

[‪Mohammad Roostaie‬ ‪]

Thank you Justin. Here is the link to access the topology 
file:https://www.dropbox.com/sh/x58tzpmg0vzkbtg/AADH_efF_s8jKx4OaHN8a7IPa?dl=0

By the way, I do not know about your advice. Can you please give me the link?
Kind regards,Mohammad

  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org 
 Sent: Monday, 29 May 2017, 0:21:10
 Subject: Re: [gmx-users] Genion error
   


On 5/28/17 3:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Hi All, when I wanted to add ions to the system, I got this error:
> Fatal error:No line with moleculetype 'SOL' found the [ molecules ] section 
> of file 'gr.top'For more information and tips for troubleshooting, please 
> check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
> However, there is 'SOL' molecule type in the [ molecules ] section of the 
> topology file. Can you please help me to solve this problem?

Upload your topology to a file-sharing service and provide the URL to access 
it. 
  There's no way to know what's going on (and I recall giving some previous 
advice about line endings - have you checked this?)

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Genion error

[‪Mohammad Roostaie‬ ‪]

Hi All, when I wanted to add ions to the system, I got this error:
Fatal error:No line with moleculetype 'SOL' found the [ molecules ] section of 
file 'gr.top'For more information and tips for troubleshooting, please check 
the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
However, there is 'SOL' molecule type in the [ molecules ] section of the 
topology file. Can you please help me to solve this problem?
Thanks,Mohammad
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Re: [gmx-users] Grompp error for graphene modeling

[‪Mohammad Roostaie‬ ‪]

Thanks Justin for your help. I will modify the force field again to model the 
particles better.
Best,Mohammad

  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org 
 Sent: Saturday, 27 May 2017, 23:20:26
 Subject: Re: [gmx-users] Grompp error for graphene modeling
  


On 5/27/17 3:33 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Hi All,
> I modeled graphene in a box of water with a peptide in the center of the box. 
> I modified the OPLS-AA force field by adding the parameters from this link to 
> the modified force field: http://chembytes.wikidot.com/grocnt. But, when I 
> want to add ions to the system, I got this warning:
> WARNING 1 [file ffbonded.itp, line 305]:  Overriding Bond parameters.
>    old:                                          0.151 292880 0.151 292880  
>new: C    C      1    0.14000  392459.2
> Actually, in the ffbonded.itp file, I put two parameters for C-C which the 
> new one referes to the graphene, and, I cannot change the names in the itp 
> file since the graphene atom names are C.Is this an important warning (May it 
> affect the stability of the system and results)? Or may I use -maxwarn?

Atom *names* and *types* are different beasts.  Types are used in 
ffnonbonded.itp and applied to the atoms found in the topology.  Atom names are 
irrelevant for parameter assignment.  But here you have introduced clearly 
conflicting parameters that will alter the behavior of the conflicting types, 
e.g. any aromatic rings in your peptide will behave incorrectly if you proceed 
with what you're doing.

In general, do not use -maxwarn unless you can clearly articulate why you're 
overriding a serious warning from grompp, not simply to make a problem go away.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Grompp error for graphene modeling

[‪Mohammad Roostaie‬ ‪]

Hi All,
I modeled graphene in a box of water with a peptide in the center of the box. I 
modified the OPLS-AA force field by adding the parameters from this link to the 
modified force field: http://chembytes.wikidot.com/grocnt. But, when I want to 
add ions to the system, I got this warning:
WARNING 1 [file ffbonded.itp, line 305]:  Overriding Bond parameters.
  old:                                          0.151 292880 0.151 292880  new: 
C     C       1    0.14000   392459.2
Actually, in the ffbonded.itp file, I put two parameters for C-C which the new 
one referes to the graphene, and, I cannot change the names in the itp file 
since the graphene atom names are C.Is this an important warning (May it affect 
the stability of the system and results)? Or may I use -maxwarn? 
Best,Mohammad

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[gmx-users] grompp error

[‪Mohammad Roostaie‬ ‪]

Hi GROMACS users,


 
I want to simulate a graphene sheet, and I want to use OPLS-AA force field. So, 
I copied the forcefield in my directory and changed some the files in it 
(ffbonded.itp, ffnonbonded.itp, atomtype.atp, aminoacids.rtp, and 
atomname2type.n2t). I used the pdb2gmx command to create the first topology and 
coordinate files with the modified OPLS-AA forcefield, then I created a box and 
solvated it with water. But, when I wanted to add ions to the box by using “gmx 
grompp -f ions.mdp -c gr_solv.gro -p gr.top -o ions.tpr”, I got this error: 


NOTE 1 [file ions.mdp]:  With Verlet lists the optimal nstlist is >= 10, with 
GPUs >= 20. Note  that with the Verlet scheme, nstlist has no effect on the 
accuracy of  your simulation.
Setting the LD random seed to 209904318
WARNING 1 [file ffbonded.itp, line 305]:  Overriding Bond parameters.
  old:                                          0.151 292880 0.151 292880  new: 
C     C       1    0.14000   392459.2
Generated 36 of the 36 non-bonded parameter combinationsGenerating 1-4 
interactions: fudge = 0.5Generated 36 of the 36 1-4 parameter 
combinations
---Program gmx grompp, 
VERSION 5.1.4Source code file: 
/home/jemmyhu/work/software/gromacs/gromacs-5.1.4/src/gromacs/gmxpreprocess/topio.c,
 line: 755
Fatal error:Syntax error - File forcefield.itp, line 18Last line read:'[ 
defaults ]'Invalid order for directive defaultsFor more information and tips 
for troubleshooting, please check the GROMACSwebsite at 
http://www.gromacs.org/Documentation/Errors

Can you please help me to solve this problem?
Thanks,Mohammad
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[gmx-users] Graphene

[‪Mohammad Roostaie‬ ‪]

Hi,
I simulated the graphene by using this link 
"http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube;. Then, I 
solvated it in water using 'gmx solvate' command. But, when I wanted to add 
ions in the media by using 'gmx grompp' command, I got this error:...ERROR 6383 
[file graphene1110v.top, line 48377]:  No default Proper Dih. types

ERROR 6384 [file graphene1110v.top, line 48378]:  No default Proper Dih. types

ERROR 6385 [file graphene1110v.top, line 48379]:  No default Proper Dih. types
Excluding 3 bonded neighbours molecule type 'graphene'Removing all charge 
groups because cutoff-scheme=Verlet
There was 1 note
---Program gmx grompp, 
VERSION 5.1.4Source code file: 
/home/jemmyhu/work/software/gromacs/gromacs-5.1.4/src/gromacs/gmxpreprocess/grompp.c,
 line: 1738
Fatal error:There were 6385 errors in input file(s)For more information and 
tips for troubleshooting, please check the GROMACSwebsite at 
http://www.gromacs.org/Documentation/Errors
Can you please help me?
Best,Mohammad
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Re: [gmx-users] Graphene modeling

[‪Mohammad Roostaie‬ ‪]

Hi Justin,
Thank you very much. It is Ok now.
Best,Mohammad

  From: Justin Lemkul <jalem...@vt.edu>
 To: Discussion list for GROMACS users <gmx-us...@gromacs.org> 
 Sent: Tuesday, 16 May 2017, 18:34:14
 Subject: Re: [gmx-users] Graphene modeling
   


On 5/16/17 7:31 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> In addition, I used this command "gmx x2top -f g.gro -o g.top -ff cnt_oplsaa
> -name CNT -noparam" and I got this error:
>
> Opening force field file ./cnt_oplsaa.ff/atomnames2types.n2t
> There are 6 name to type translations in file ./cnt_oplsaa.ff
> Generating bonds from distances...
> atom 46
> There are 1 different atom types in your sample
> Generating angles and dihedrals from bonds...
> Segmentation fault
>

Are you using the latest version of GROMACS?  There was an x2top seg fault 
fixed 
a few versions ago so using 2016.3 may be necessary here.

-Justin

> Best
> Mohammad
>
>
> ----
> *From:* ‪Mohammad Roostaie‬ ‪ <mohammad.r0...@yahoo.com>
> *To:* Justin Lemkul <jalem...@vt.edu>; gmx-us...@gromacs.org
> *Sent:* Tuesday, 16 May 2017, 13:59:29
> *Subject:* Re: [gmx-users] Graphene modeling
>
> Thank you Justin,
>
> Actually, I want to simulate a small box of water with graphene and protein. 
> You
> mean that I should just build and put the .n2t file in the directory where I
> want to run the system, and no other files are required or should not be 
> changed.
>
> I used the files specified in this
> link: http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
> <http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube.>
>
> For example, for .n2t file:
>
> |; Oplsaa-based n2t for carbon-based structures such as CNTs and graphenes ;
> Andrea Minoia H HJ 0.00 1.008 1 C 0.109 ;Hydrogen C CJ 0.00 12.011 3 C 0.142 H
> 0.109 H 0.109 ;Periferic C C CJ 0.00 12.011 3 C 0.142 C 0.142 H 0.108 
> ;Periferic
> C C CJ 0.00 12.011 1 C 0.142 ;Internal/periodic C C CJ 0.00 12.011 2 C 0.142 C
> 0.142 ;Internal/periodic C C CJ 0.00 12.011 3 C 0.142 C 0.142 C 0.142
> ;Internal/periodic C|
>
>
> Thanks,
> Mohammad
> 
> *From:* Justin Lemkul <jalem...@vt.edu>
> *To:* gmx-us...@gromacs.org; ‪Mohammad Roostaie‬ ‪ <mohammad.r0...@yahoo.com>
> *Sent:* Monday, 15 May 2017, 16:45:19
> *Subject:* Re: [gmx-users] Graphene modeling
>
>
>
> On 5/14/17 9:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:
>> Hi GROMACS users,
>>
>>
>>
>> I want to model a graphene sheet. I used the instruction stated in link
> http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube.
> <http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube.>I put the
> cnt_oplsaa.ff folder in the directory where I want to run the rest of the 
> work.
> Also, I rename the residues of the graphene to “CJ” and the atoms to “C”. but,
> when I want to use “gmx x2top”, I get the error that says it cannot find any
> forcefield type for the atoms. Can you please help me to figure this out?
>
>>
>
> Since all you have are C atoms, this should require only a one-line .n2t file
> (or addition to an existing one) that specifies the proper equilibrium bond
> length for C-C in your structure.  Without seeing your .n2t file and the x2top
> screen output, there's nothing to suggest other than your .n2t file is somehow
> inadequate for what you're trying to do.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu <mailto:jalem...@outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
>
> ==
>
>
>
>

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Graphene modeling

[‪Mohammad Roostaie‬ ‪]

In addition, I used this command "gmx x2top -f g.gro -o g.top -ff cnt_oplsaa 
-name CNT -noparam" and I got this error:
Opening force field file ./cnt_oplsaa.ff/atomnames2types.n2tThere are 6 name to 
type translations in file ./cnt_oplsaa.ffGenerating bonds from distances...atom 
46There are 1 different atom types in your sampleGenerating angles and 
dihedrals from bonds...Segmentation fault BestMohammad 

      From: ‪Mohammad Roostaie‬ ‪ <mohammad.r0...@yahoo.com>
 To: Justin Lemkul <jalem...@vt.edu>; gmx-us...@gromacs.org 
 Sent: Tuesday, 16 May 2017, 13:59:29
 Subject: Re: [gmx-users] Graphene modeling
   
Thank you Justin,
Actually, I want to simulate a small box of water with graphene and protein. 
You mean that I should just build and put the .n2t file in the directory where 
I want to run the system, and no other files are required or should not be 
changed. 
I used the files specified in this link: 
http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
For example, for .n2t file:; Oplsaa-based n2t for carbon-based structures such 
as CNTs and graphenes
; Andrea Minoia
HHJ0.00   1.008  1C 0.109  ;Hydrogen
CCJ0.00  12.011  3C 0.142   H 0.109   H 0.109 ;Periferic C
CCJ0.00  12.011  3C 0.142   C 0.142   H 0.108 ;Periferic C
CCJ0.00  12.011  1C 0.142  
;Internal/periodic C
CCJ0.00  12.011  2C 0.142   C 0.142
;Internal/periodic C
CCJ0.00  12.011  3C 0.142   C 0.142   C 0.142 
;Internal/periodic C
Thanks,Mohammad  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org; ‪Mohammad Roostaie‬ ‪ <mohammad.r0...@yahoo.com> 
 Sent: Monday, 15 May 2017, 16:45:19
 Subject: Re: [gmx-users] Graphene modeling
  


On 5/14/17 9:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Hi GROMACS users,
>
>
>
> I want to model a graphene sheet. I used the instruction stated in link 
> http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube. I put the 
> cnt_oplsaa.ff folder in the directory where I want to run the rest of the 
> work. Also, I rename the residues of the graphene to “CJ” and the atoms to 
> “C”. but, when I want to use “gmx x2top”, I get the error that says it cannot 
> find any forcefield type for the atoms. Can you please help me to figure this 
> out?
>

Since all you have are C atoms, this should require only a one-line .n2t file 
(or addition to an existing one) that specifies the proper equilibrium bond 
length for C-C in your structure.  Without seeing your .n2t file and the x2top 
screen output, there's nothing to suggest other than your .n2t file is somehow 
inadequate for what you're trying to do.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==


   

   
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Re: [gmx-users] Graphene modeling

[‪Mohammad Roostaie‬ ‪]

Thank you Justin,
Actually, I want to simulate a small box of water with graphene and protein. 
You mean that I should just build and put the .n2t file in the directory where 
I want to run the system, and no other files are required or should not be 
changed. 
I used the files specified in this link: 
http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
For example, for .n2t file:; Oplsaa-based n2t for carbon-based structures such 
as CNTs and graphenes
; Andrea Minoia
HHJ0.00   1.008  1C 0.109  ;Hydrogen
CCJ0.00  12.011  3C 0.142   H 0.109   H 0.109 ;Periferic C
CCJ0.00  12.011  3C 0.142   C 0.142   H 0.108 ;Periferic C
CCJ0.00  12.011  1C 0.142  
;Internal/periodic C
CCJ0.00  12.011  2C 0.142   C 0.142
;Internal/periodic C
CCJ0.00  12.011  3C 0.142   C 0.142   C 0.142 
;Internal/periodic C
Thanks,Mohammad  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org; ‪Mohammad Roostaie‬ ‪ <mohammad.r0...@yahoo.com> 
 Sent: Monday, 15 May 2017, 16:45:19
 Subject: Re: [gmx-users] Graphene modeling
   


On 5/14/17 9:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Hi GROMACS users,
>
>
>
> I want to model a graphene sheet. I used the instruction stated in link 
> http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube. I put the 
> cnt_oplsaa.ff folder in the directory where I want to run the rest of the 
> work. Also, I rename the residues of the graphene to “CJ” and the atoms to 
> “C”. but, when I want to use “gmx x2top”, I get the error that says it cannot 
> find any forcefield type for the atoms. Can you please help me to figure this 
> out?
>

Since all you have are C atoms, this should require only a one-line .n2t file 
(or addition to an existing one) that specifies the proper equilibrium bond 
length for C-C in your structure.  Without seeing your .n2t file and the x2top 
screen output, there's nothing to suggest other than your .n2t file is somehow 
inadequate for what you're trying to do.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==


   
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[gmx-users] Graphene modeling

[‪Mohammad Roostaie‬ ‪]

Hi GROMACS users,


 
I want to model a graphene sheet. I used the instruction stated in link 
http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube. I put the 
cnt_oplsaa.ff folder in the directory where I want to run the rest of the work. 
Also, I rename the residues of the graphene to “CJ” and the atoms to “C”. but, 
when I want to use “gmx x2top”, I get the error that says it cannot find any 
forcefield type for the atoms. Can you please help me to figure this out?


 
Best,

Mohammad

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Re: [gmx-users] Analaysis

[‪Mohammad Roostaie‬ ‪]

Hi Amir,
I used these commands for installing:
sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O 
/usr/local/bin/dssp

sudo add-apt-repository ppa:sfleischmann/tcbsys

sudo apt-get update

sudo apt-get install dssp


and these for running:
do_dssp -f md.xtc -s md.tpr -o dsso.xpm -sc dssp.xvg

xpm2ps  -f dssp.xpm -o dssp.eps -di ps.m2p

ps2pdf dssp.eps dssp.pdf


Best,Mohammad
  From: Amir Zeb <zebami...@gmail.com>
 To: gmx-us...@gromacs.org 
 Sent: Monday, 12 December 2016, 6:05:23
 Subject: Re: [gmx-users] Analaysis
   
hello mohammad

can you please let me know how to install do_dssp on my gromacs 5.0.6
we have downloaded the package but we could not install
please help

thanks

On Dec 11, 2016 11:45 PM, "Justin Lemkul" <jalem...@vt.edu> wrote:

>
>
> On 12/11/16 1:01 AM, ‪Mohammad Roostaie‬ ‪ wrote:
>
>>
>>
>>
>> Hi Gromacs users, I want to obtain the percentage of helicity of a peptide
>> with respect to time after the simulation, how can I get it? I used the
>> "gmx
>> helix" and "gmx do_dssp" commands, but I could not get it. In addition, I
>>
>
> The last line in scount.xvg from gmx do_dssp gives you this.
>
> want to get the number of clusters and contact area of two particles with
>> respect to time, and I used "gmx clustsize" and "gmx mindist" commands,
>> but I
>> still cannot get these factors. can you please help me figure this out?
>> Thank
>>
>
> gmx clustsize has output options for number of clusters, cluster size,
> distribution, etc.
>
> If you want contact area, use gmx sasa with appropriate index groups.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] Analaysis

[‪Mohammad Roostaie‬ ‪]

Thank you very much Justin
Best,Mohammad

  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org 
 Sent: Sunday, 11 December 2016, 18:15:01
 Subject: Re: [gmx-users] Analaysis
   


On 12/11/16 1:01 AM, ‪Mohammad Roostaie‬ ‪ wrote:
>
>
>
> Hi Gromacs users, I want to obtain the percentage of helicity of a peptide
> with respect to time after the simulation, how can I get it? I used the "gmx
> helix" and "gmx do_dssp" commands, but I could not get it. In addition, I

The last line in scount.xvg from gmx do_dssp gives you this.

> want to get the number of clusters and contact area of two particles with
> respect to time, and I used "gmx clustsize" and "gmx mindist" commands, but I
> still cannot get these factors. can you please help me figure this out? Thank

gmx clustsize has output options for number of clusters, cluster size, 
distribution, etc.

If you want contact area, use gmx sasa with appropriate index groups.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Analaysis

[‪Mohammad Roostaie‬ ‪]

   
Hi Gromacs users,
I want to obtain the percentage of helicity of a peptide with respect to time 
after the simulation, how can I get it? I used the "gmx helix" and "gmx 
do_dssp" commands, but I could not get it.
In addition, I want to get the number of clusters and contact area of two 
particles with respect to time, and I used "gmx clustsize" and "gmx mindist" 
commands, but I still cannot get these factors. can you please help me figure 
this out?
Thank you,Mohammad

   
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[gmx-users] Time of NPT and NVT running

[‪Mohammad Roostaie‬ ‪]

Hi everybody,


 
I am simulating a peptide in a box of water with differentconcentration of 
water. The system has about 14000 molecules of water. The runningof NVT and NPT 
simulation last about 1 hour with the time step of 100 ps. When therunning is 
completed I check the diagram of temperature and pressure and theyare ok and 
stable. Now I don’t know whether the time of running (about 1 hour)is correct 
or it should be longer than an hour.


Thank you, Mohammad.
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