[gmx-users] unstable system

[Shima Arasteh]

Hi all,

 I have a system of peptide/POPC/water/ions. The energy minimization and NVT 
steps has passed successfully. I ran NPT step for around 10 ns with restraints 
of protein and P atoms at first nano seconds and then removing them gradually. 
I tried to go on MDRUN. I did not remove restraint of protein atoms completely 
and they are still restrained. When I run the mdrun command, I get error of "X 
particles communicated to PME node Y are more than a cell length out of the 
domain decomposition cell of their charge group" .
I know this error means an unstable system. When I visualized the written pdb 
files, I see some popc hydrogen atoms are broken and located between two 
leaflets which are separated by a gap. The protein seems ok, however I  don't 
get many pdb files to see.


As what I see in Diagnosing unstable system web page,
1. it would be beneficial if one see what part of the system is unstable in 
first steps. As I saw, the unstable "POPC hydrogen atoms" are not fine.
2. The single molecules are supposed to examine in water or vacuum too. I have 
passed this step successfully.
3. I have not ignored any warning during the last steps.
4. And my mdp files to run md is as follow:

integrator    = md        
dt        = 0.002      
nsteps        = 500    


ns_type        = grid        
nstlist        = 5       
rlist        = 1.2       
rlistlong   = 1.4
rcoulomb    = 1.2        
rvdw        = 1.2       
pbc        = xyz        
vdwtype = switch
rvdw_switch = 0.1
; Parameters for treating bonded interactions
continuation    = yes       
constraint_algorithm = LINCS    NCS / SHAKE)
constraints    = all-bonds    )
lincs_iter    = 1        
lincs_order    = 4      

; Parameters for treating electrostatic interactions
coulombtype    = PME        ; Long range electrostatic interactions treatment 
(cut-off, Ewald, PME)
pme_order    = 4        ; Interpolation order for PME (cubic interpolation is 
represented by 4)
fourierspacing    = 0.16        ; Maximum grid spacing for FFT grid using PME 
(nm)

; Temperature coupling parameters
tcoupl        = Nose-Hoover        
tc-grps        = Protein_POPC Water_and_ions        ; Define groups to be 
coupled separately to temperature bath
tau_t        = 0.5    0.5         ; Group-wise coupling time constant (ps)
ref_t        = 310     310        ; Group-wise reference temperature (K)

; Pressure coupling parameters
pcoupl        = Parrinello-Rahman      
pcoupltype    = semiisotropic            
tau_p        = 2.0                
ref_p        = 1.01325 1.01325       
compressibility = 4.5e-5    4.5e-5 

; Miscellaneous control parameters
; Dispersion correction
DispCorr    = EnerPres      
; Initial Velocity Generation
gen_vel        = no          
; Centre of mass (COM) motion removal relative to the specified groups
nstcomm        = 1           y (steps)
comm_mode    = Linear      
comm_grps    =Protein_POPC Water_and_ions    ; COM removal relative to the 
specified groups

 Would you please let me know if these happen due to an improper equilibration? 
Do I need to extend the NPT step? Would that fix it?

Thanks in advance. I appreciate your suggestions.
  

Sincerely,
Shima
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Re: [gmx-users] Improve performance

[Justin Lemkul]

On Sat, Apr 6, 2013 at 9:11 PM, 陈照云  wrote:

> Hi!
> I have 6 nodes. Each node has two CPUs,12 cores totally.
> How should I set the options like -rdd,-rcon,-dds,-gcom to improve the
> performance?
>

Those options will have a significantly smaller impact on performance than
other factors like .mdp settings (algorithms used) and system size (number
of atoms).

-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Improve performance

[陈照云]

Hi!
I have 6 nodes. Each node has two CPUs,12 cores totally.
How should I set the options like -rdd,-rcon,-dds,-gcom to improve the
performance?
Thanks!
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Re: [gmx-users] Adding second solvent

[Justin Lemkul]

On Sat, Apr 6, 2013 at 5:37 PM, Juliette N.  wrote:

> Dear all,
>
> I need to add 100 molecules of a second solvent to my polymer. I do this in
> two solvation steps as below:
>
> genbox -cp Solute.gro -ci Solvent1.gro -o solute-solvent1.gro -nmol 500
>
> genbox -cp solute-solvent1.gro -ci Solvent2.gro -o
> solute-solvent1-solvent2.gro
> -nmol 100
>
> 1- Is this the correct of adding two solvents to a solute? or This has to
> be done in one step.
>
>
It is not possible to use the -ci -nmol mechanism with multiple molecules
in one step.


> 2- Does the box size (last line in gro) of solvent affect the final box
> size of the solute-solvent1.gro? I mean do I need to keep size of
> Solvent1.gro
> or Solvent2.gro as small as possible to avoid huge box for
> solute-solvent1.gro
> or solute-solvent1-solvent2.gro?
>
>
Did your approach work? The box vectors in the inserted coordinate file are
irrelevant.


> 3- In mdp file do I have to assign the uniform solution temperature to each
> component or that is sufficient to have tc-grps =  System  ?
>
>
Technically, coupling the system together is the only correct way to treat
thermostats. In practice, the exact implementation depends on the chosen
thermostat algorithm. See extensive discussions in the list archive on this
topic.

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Adding second solvent

[Juliette N.]

Dear all,

I need to add 100 molecules of a second solvent to my polymer. I do this in
two solvation steps as below:

genbox -cp Solute.gro -ci Solvent1.gro -o solute-solvent1.gro -nmol 500

genbox -cp solute-solvent1.gro -ci Solvent2.gro -o solute-solvent1-solvent2.gro
-nmol 100

1- Is this the correct of adding two solvents to a solute? or This has to
be done in one step.

2- Does the box size (last line in gro) of solvent affect the final box
size of the solute-solvent1.gro? I mean do I need to keep size of Solvent1.gro
or Solvent2.gro as small as possible to avoid huge box for solute-solvent1.gro
or solute-solvent1-solvent2.gro?

3- In mdp file do I have to assign the uniform solution temperature to each
component or that is sufficient to have tc-grps =  System  ?

-
Thanks for your comments,
Have a great weekend
J.
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Re: [gmx-users] fail to pull

[Justin Lemkul]

On Sat, Apr 6, 2013 at 2:47 PM, Albert  wrote:

> Dear:
>
>  I am trying to pull my ligand outside of the binding pocket with
> following configurations:
>
> title   = Umbrella pulling simulation
> define  = -DPOSRES
> ; Pull code
> pull= umbrella
> pull_geometry   = distance  ; simple distance increase
> pull_dim= Y N N
> pull_start  = yes   ; define initial COM distance > 0
> pull_ngroups= 1
> pull_group0 = Protein
> pull_group1 = LIG
> pull_rate1  = 0.001  ; 0.01 nm per ps = 10 nm per ns
> pull_k1 = 1000  ; kJ mol^-1 nm^-2
>
> Tcoupl  = v-rescale
> tc_grps = Protein_LIG   Water_and_ions
> tau_t   = 0.5   0.5
> ref_t   = 310   310
> ; Pressure coupling is on
> Pcoupl  = Parrinello-Rahman
> pcoupltype  = isotropic
> tau_p   = 1.0   1.0
> compressibility = 4.5e-5
> ref_p   = 1.0 1.0
> refcoord_scaling = com
> ; Generate velocities is off
> gen_vel = no
> ; Periodic boundary conditions are on in all directions
> pbc = xyz
> ; Long-range dispersion correction
> DispCorr= EnerPres
>
>
>
> It is quite strange, the ligand is still in place and not outside the
> pocket at the end of simulations. I am just wondering where is the problem?
>
>
Hard to tell. Does your ligand have a suitable exit pathway exactly aligned
along the x-axis? Have you tried increasing the pull rate? How long is the
simulation? I don't even see nsteps in the above .mdp file. How about
increasing the force constant? Is the vector connecting the COM of the
entire protein and the COM of the ligand suitable for describing the exit
pathway?

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] fail to pull

[Albert]

Dear:

 I am trying to pull my ligand outside of the binding pocket with 
following configurations:


title   = Umbrella pulling simulation
define  = -DPOSRES
; Pull code
pull= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim= Y N N
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = Protein
pull_group1 = LIG
pull_rate1  = 0.001  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1 nm^-2

Tcoupl  = v-rescale
tc_grps = Protein_LIG   Water_and_ions
tau_t   = 0.5   0.5
ref_t   = 310   310
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 1.0   1.0
compressibility = 4.5e-5
ref_p   = 1.0 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres



It is quite strange, the ligand is still in place and not outside the 
pocket at the end of simulations. I am just wondering where is the problem?


thank you very much
best
Albert

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Re: [gmx-users] Restarting minimization

[Justin Lemkul]

On Sat, Apr 6, 2013 at 2:23 PM, Juan Antonio Raygoza Garay  wrote:

> Hi, i'm new to grimaces and want to run a minimization process in parts,
> but i'm having problems extracting the last frame, when i try the following
> command:
>
> trjconv -s em-vac${ID}.tpr -f em-vac${ID}.trr -o mintmp.pdb -e 0
>
>
The last frame is always written by mdrun when the process completes.
Moreover, your command will extract the first frame (-e 0 is "ending at
zero time), not the last.


> it returns no data, if i try 11 in the frame number it prints out  a
> model, but when trying to run mintmp.pdb, i get the following error:
>
> Fatal error:
> There is no domain decomposition for 8 nodes that is compatible with the
> given box and a minimum cell size of 23.38 nm
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition
>
> what am i doing wrong? or is there a tutorial where someone does this.
>
>
Intermediate frames that are stored in trajectories have molecules broken
across periodic boundaries. In principle, that shouldn't be an issue, but
the error message suggests that's precisely the problem. trjconv -pbc mol
will take care of that problem. Domain decomposition cells should be on the
order of the largest cutoff.

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Restarting minimization

[Juan Antonio Raygoza Garay]

Hi, i'm new to grimaces and want to run a minimization process in parts, but 
i'm having problems extracting the last frame, when i try the following command:

trjconv -s em-vac${ID}.tpr -f em-vac${ID}.trr -o mintmp.pdb -e 0

it returns no data, if i try 11 in the frame number it prints out  a model, but 
when trying to run mintmp.pdb, i get the following error:

Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the given 
box and a minimum cell size of 23.38 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition

what am i doing wrong? or is there a tutorial where someone does this.

Thanks


em-vac-pbe.mdp


; Define can be used to control processes
define = -DFLEXIBLE ; Use flexible water model
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 500.0 ; Stop minimization when the maximum force < 1.0 kJ/mol
nsteps = 100 ; Maximum number of (minimization) steps to perform
nstenergy = 1 ; Write energies to disk every nstenergy steps
energygrps = System ; Which energy group(s) to write to disk
nstlist = 1 ; Frequency to update the neighbor list
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Treatment of long range electrostatic interactions
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
constraints = none ; Bond types to replace by constraints
pbc = xyz ; Periodic Boundary Conditions--
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[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

[Dr. Vitaly Chaban]

In systems of such kind, everything will depend on the atom of the ligand,
which coordinated by copper ion.

Perform ab initio geometry optimization and find the optimal distance. Then
adjust sigma(s).

Dr. Vitaly Chaban







There is a copper ion with four ligands in my system. I am going to
> study this system using MD simulations.
> For the vdW parameters, R*=1.74 angstrom and epsilon=1.14 kcal.mol from
> one paper will be used in our
> simulations. I already found the parameters of copper ion (Cu2+) in the
> OPLS-AA/L force field files:
> sigma= 2.08470e-01, epsilon=4.76976e+00, which are for Cu2+ without
> ligands. The two epsilon are the same,
> just with different units.
>
> My question is that I do not know how to convert the vdW radius to
> sigma. I found that the vdw radius of copper is
> 1.4 angstrom, and the sigma in the force field file is 2.08470e-01.
> Could someone tell me how to do the converting?
>
> Thanks very much!
>
>
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Re: [gmx-users] amber99 with berger's lipids

[Justin Lemkul]

On Sat, Apr 6, 2013 at 10:46 AM, Albert  wrote:

> On 04/06/2013 04:29 PM, Justin Lemkul wrote:
>
>> And what was your basis for that decision?  What makes you think that
>> AMBER99 can even be combined with the Berger lipid force field?
>>
>> -Justin
>>
>
>
> I think he probably read this paper which suggest the combination of Amber
> FF and Berger lipids FF:
>
> http://pubs.acs.org/doi/abs/**10.1021/ct200491c
>

Fair enough. I wasn't aware of that one. But if that's the case, then I
suggest James have another read through it, since the cutoffs are described
explicitly, thus answering his original question.

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] amber99 with berger's lipids

[Albert]

On 04/06/2013 04:29 PM, Justin Lemkul wrote:

And what was your basis for that decision?  What makes you think that
AMBER99 can even be combined with the Berger lipid force field?

-Justin



I think he probably read this paper which suggest the combination of 
Amber FF and Berger lipids FF:


http://pubs.acs.org/doi/abs/10.1021/ct200491c
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[gmx-users] How to set the sigma and epsilon for Cu2+ in OPLS-AA/L force field

[fantasticqhl]

Dear GMX users,

There is a copper ion with four ligands in my system. I am going to 
study this system using MD simulations.
For the vdW parameters, R*=1.74 angstrom and epsilon=1.14 kcal.mol from 
one paper will be used in our
simulations. I already found the parameters of copper ion (Cu2+) in the 
OPLS-AA/L force field files:
sigma= 2.08470e-01, epsilon=4.76976e+00, which are for Cu2+ without 
ligands. The two epsilon are the same,

just with different units.

My question is that I do not know how to convert the vdW radius to 
sigma. I found that the vdw radius of copper is
1.4 angstrom, and the sigma in the force field file is 2.08470e-01. 
Could someone tell me how to do the converting?


Thanks very much!


All the best,
Qinghua
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Re: [gmx-users] amber99 with berger's lipids

[Justin Lemkul]

On Sat, Apr 6, 2013 at 8:45 AM, James Starlight wrote:

> That paper suggests of using 1.0 nm for all cut-offs
> http://pubs.acs.org/doi/abs/10.1021/ct200491c
>
> that seems strange to me because with gromos-56 I've used 1.2 nm cutoffs.
>
>
And what was your basis for that decision?  What makes you think that
AMBER99 can even be combined with the Berger lipid force field?

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] problem with REMD

[Justin Lemkul]

On Sat, Apr 6, 2013 at 7:17 AM, Shine A  wrote:

> Respected Sir,
>
>  Now I am trying an REMD simulation on a peptide in
> cluster. The command line I used as follows
>
> mpirun -np 6 /usr/local/gromacs/bin/mdrun_mpi -s sd_.tpr -multi 2
> -replex 1000 -reseed 175320
>
> But this command line getting error like this
>
> Wrote pdb files with previous and current coordinates
> [lilavati:27635] *** Process received signal ***
> [lilavati:27635] Signal: Segmentation fault (11)
> [lilavati:27635] Signal code: Address not mapped (1)
> [lilavati:27635] Failing at address: 0x2aaab438b8a8
> [lilavati:27635] [ 0] /lib64/libpthread.so.0 [0x357c00e4c0]
> [lilavati:27635] [ 1]
> /usr/local/gromacs/lib/libmd_mpi_d.so.6(gb_bonds_tab+0x246)
> [0x2b8f12dc1eb6]
> [lilavati:27635] [ 2]
> /usr/local/gromacs/lib/libmd_mpi_d.so.6(calc_gb_forces+0x110)
> [0x2b8f12dc18f0]
> [lilavati:27635] [ 3]
> /usr/local/gromacs/lib/libmd_mpi_d.so.6(do_force_lowlevel+0x5b5)
> [0x2b8f12d92ab5]
> [lilavati:27635] [ 4]
> /usr/local/gromacs/lib/libmd_mpi_d.so.6(do_force+0xd82) [0x2b8f12df2622]
> [lilavati:27635] [ 5] /usr/local/gromacs/bin/mdrun_mpi(do_md+0x5913)
> [0x41cbb3]
> [lilavati:27635] [ 6] /usr/local/gromacs/bin/mdrun_mpi(mdrunner+0x12ae)
> [0x41704e]
> [lilavati:27635] [ 7] /usr/local/gromacs/bin/mdrun_mpi(main+0xb4d)
> [0x41da8d]
> [lilavati:27635] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4)
> [0x357b41d974]
> [lilavati:27635] [ 9] /usr/local/gromacs/bin/mdrun_mpi(do_cg+0x191)
> [0x407d79]
> [lilavati:27635] *** End of error message ***
> --
> mpirun noticed that process rank 0 with PID 27635 on node lilavati exited
> on signal 11 (Segmentation fault).
> --
>
>
> Why this error coming here?Can you give a solution for this? Thanks in
> advance
>

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] where is gromos54a7_lipid FF?

[Reid Van Lehn]

It's available in Gromacs format from the Automatic Topology Builder
website:

http://compbio.biosci.uq.edu.au/atb/index.py?tab=forceField_tab


On Sat, Apr 6, 2013 at 6:38 AM, Albert  wrote:

> Hello:
>
>  I saw lots of people is using gromos54a7_lipid FF and I search the
> gromacs webiste, but didn't find it. Would anybody tell me where can we
> obtain it?
>
> THX
>
> Albert
> --
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-- 
Reid Van Lehn
NSF/MIT Presidential Fellow
Alfredo Alexander-Katz Research Group
Ph.D Candidate - Materials Science
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[gmx-users] FEP + Ham. REMD

[Yuri Garmay]

Hi all!

I have a problem. So as it can be seen in the theme I am trying to improve
sampling of free energy calculating simulation by using replica exchange.
In the gmx4.6 it is simple while using FEP technique, but does not
implemented for umbrella sampling. But I want evaluate potential of mean
force between two flexible molecules, so I have decided to do this with
FEP+REMD.

It is desirable to select distance between the mass centres as a reaction
coordinate, but FEP has to do with bonds or constraints between single
atoms. Luckily there virtual sites are possible to define in gromacs. So I
have a thought of using it.

But I have never been using virtual sites and so have some questions.
I  introduced two virtual sites in topology with these lines:


*.top:
[ atomtypes ]
;name mass charge ptype sigma epsilon
DD 0.0 0.0 V 0 0 ; nb interaction off?

[ implicit_genborn_params ]
; Atomtype sar st pi gbr hct
DD 0.0 0 0.0 0.0 0.0 ; interaction with solvent off?

[ atoms ]
...some lines .
   111 DD  9DDD DD111  0
   112 DD 10DDD DD112  0

[ virtual_sitesn ]
; Site from funct a d
1112   12 ... ; virtual site at mass centre of some groupe
1122   82   83 ...

[ bonds ]

  111   112 6   0.3   10001.3
1000 ; harmonic bond


*.gro:
9DDD DD  111   0.000   0.000   0.000 /// position have to be
determined automatically?
   10DDD DD  112   0.000   0.000   0.000
--

The energy minimization showed correct constraint length at first sight.
But does this method solve problem I have? I will be very much appreciated
if someone experienced explains me whether this is correct or there are
pitfalls at this way.


-- 
Best regards,
Yuri
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Re: [gmx-users] amber99 with berger's lipids

[James Starlight]

That paper suggests of using 1.0 nm for all cut-offs
http://pubs.acs.org/doi/abs/10.1021/ct200491c

that seems strange to me because with gromos-56 I've used 1.2 nm cutoffs.

James

2013/4/6 Mark Abraham 

> How about reading the literature on combining AMBER and Berger? :-)
>
> Mark
>
> On Sat, Apr 6, 2013 at 8:24 AM, James Starlight  >wrote:
>
> > Dear Gromacs Users!
> >
> >
> > I'm looking for cut-offs parameters which would be suitable for the
> > simulation of the membrane proteins (bergers united-atom lipids) with the
> > amber-99 force fields (full-atomic protein representation). I'd be
> thankful
> > to anyone who can provide me with such cut-offs for vdw as well as
> coulomb
> > interactions for that force field.
> >
> >
> >
> > James
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
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[gmx-users] problem with REMD

[Shine A]

Respected Sir,

 Now I am trying an REMD simulation on a peptide in
cluster. The command line I used as follows

mpirun -np 6 /usr/local/gromacs/bin/mdrun_mpi -s sd_.tpr -multi 2
-replex 1000 -reseed 175320

But this command line getting error like this

Wrote pdb files with previous and current coordinates
[lilavati:27635] *** Process received signal ***
[lilavati:27635] Signal: Segmentation fault (11)
[lilavati:27635] Signal code: Address not mapped (1)
[lilavati:27635] Failing at address: 0x2aaab438b8a8
[lilavati:27635] [ 0] /lib64/libpthread.so.0 [0x357c00e4c0]
[lilavati:27635] [ 1]
/usr/local/gromacs/lib/libmd_mpi_d.so.6(gb_bonds_tab+0x246) [0x2b8f12dc1eb6]
[lilavati:27635] [ 2]
/usr/local/gromacs/lib/libmd_mpi_d.so.6(calc_gb_forces+0x110)
[0x2b8f12dc18f0]
[lilavati:27635] [ 3]
/usr/local/gromacs/lib/libmd_mpi_d.so.6(do_force_lowlevel+0x5b5)
[0x2b8f12d92ab5]
[lilavati:27635] [ 4]
/usr/local/gromacs/lib/libmd_mpi_d.so.6(do_force+0xd82) [0x2b8f12df2622]
[lilavati:27635] [ 5] /usr/local/gromacs/bin/mdrun_mpi(do_md+0x5913)
[0x41cbb3]
[lilavati:27635] [ 6] /usr/local/gromacs/bin/mdrun_mpi(mdrunner+0x12ae)
[0x41704e]
[lilavati:27635] [ 7] /usr/local/gromacs/bin/mdrun_mpi(main+0xb4d)
[0x41da8d]
[lilavati:27635] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4)
[0x357b41d974]
[lilavati:27635] [ 9] /usr/local/gromacs/bin/mdrun_mpi(do_cg+0x191)
[0x407d79]
[lilavati:27635] *** End of error message ***
--
mpirun noticed that process rank 0 with PID 27635 on node lilavati exited
on signal 11 (Segmentation fault).
--


Why this error coming here?Can you give a solution for this? Thanks in
advance
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[gmx-users] where is gromos54a7_lipid FF?

[Albert]

Hello:

 I saw lots of people is using gromos54a7_lipid FF and I search the 
gromacs webiste, but didn't find it. Would anybody tell me where can we 
obtain it?


THX

Albert
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[gmx-users] nstxout, nstvout, . . .

[dina dusti]

Thanks from your help.

Best Regards
Dina





 From: Mark Abraham 
To: dina dusti ; Discussion list for GROMACS users 
 
Sent: Saturday, April 6, 2013 1:27 PM
Subject: Re: [gmx-users] nstxout, nstvout, . . .
 

Only you can judge that, because only you know what you are trying to observe.

Mark


On Sat, Apr 6, 2013 at 10:54 AM, dina dusti  wrote:


>
>
>
>
>
>Dear Mark and Chandan kumar Choudhury
>Thank you very much from your answers. May I know what is the best of 
>frequency to write the output (In MARTINI), Please?
>Best Regards
>Dina
>
>
>
>
>
>On Sat, Apr 6, 2013 at 8:25 AM, Chandan Choudhury  wrote:
>
>You need to re submit the jobs, with decreased time.
>>
>
>And next time check with the manual and consider your needs before making 
>arbitrary choices :-)
>
>Mark
> 
>
>>
>>--
>>Chandan kumar Choudhury
>>NCL, Pune
>>INDIA
>>
>>
>>
>>On Sat, Apr 6, 2013 at 11:20 AM, dina dusti  wrote:
>>
>>> Dear Specialists
>>>
>>>
>>> I am a beginner at Gromacs. I work with MARTINI CG force field.
>>>
>>> I selected 5 for
>>>
>>> nstxout        = 5
>>> nstvout        = 5
>>> nstenergy    = 5
>>> nstlog        = 5
>>> nstxtcout                = 5
>>>
>>> and my jobs have been finished.
>>>
>>> I found that this time is very large. Is there a way for correct this
>>> time? Or, should I do these jobs again?!
>>> May I ask you to help me, Please?
>>> Best Regards
>>> Dina
>>>
>>> --
>>> gmx-users mailing list    gmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>> www interface or send it to gmx-users-requ...@gromacs.org.
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>>>
>>--
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Re: [gmx-users] Topology file-residue unknown

[Mark Abraham]

On Sat, Apr 6, 2013 at 5:56 AM, Juliette N.  wrote:

> Thank you Justin. I have now the topology. I have a quick question
> regarding atom types. I used opls_143 and opls_144 for C and H of ethylene
> respec in rtp. However, in VMD I dont see double bonds C=C. I though maybe
> these are not the proper atomtypes for H2C=CH2.
>

http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds

Mark


>
> rtp entry:
>
> [ atoms ]
>C1opls_143-0.1201
>H11   opls_144 0.0601
>H12   opls_144 0.0601
>C2opls_143-0.1202
>H21   opls_144 0.0602
>H22   opls_144 0.0602
>
> >From atomtypes.atp
>
> opls_141   12.01100  ; alkene C (R2-C=)
>  opls_142   12.01100  ; alkene C (RH-C=)
> * opls_143   12.01100  ; alkene C (H2-C=)
>  opls_1441.00800  ; alkene H (H-C=)*
>
> Did I select the correct atomtypes?
> Thanks many times!
>
>
>
>
> On 4 April 2013 18:23, Justin Lemkul  wrote:
>
> >
> >
> > On 4/4/13 6:17 PM, Juliette N. wrote:
> >
> >> Hi Justin,
> >>
> >> Thanks a lot for your message. I am petrified why pdb2gmx is not
> >> recognizing the residue ETY. This the first residue added to
> ffoplsaa.rtp
> >> but as you may see below it is not read from rtp.
> >>
> >> I am sure this residue is added to ffoplsaa.rtp which is existing in the
> >> working directory:
> >>
> >> [ ETY ]
> >>   [ atoms ]
> >> C1opls_143-0.1201
> >> H11   opls_144 0.0601
> >> H12   opls_144 0.0601
> >> C2opls_143-0.1202
> >> H21   opls_144 0.0602
> >> H22   opls_144 0.0602
> >>
> >> [ bonds ]
> >> C1H11
> >> C1H12
> >> C1C2
> >> C2H21
> >> C2H22
> >>;C2C1
> >>
> >> Then I issue:
> >>
> >> pdb2gmx -f Ethylene.gro -o GRO.gro -p Ethylene.top -ff oplsaa
> >>   :-)  G  R  O  M  A  C  S  (-:
> >>
> >>GROwing Monsters And Cloning Shrimps
> >>
> >>  :-)  VERSION 4.5.4  (-:
> >>
> >> Using the Oplsaa force field in directory oplsaa.ff
> >>
> >> Opening force field file
> >> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**watermodels.dat
> >>
> >> Select the Water Model:
> >>   1: TIP4P  TIP 4-point, recommended
> >>   2: TIP3P  TIP 3-point
> >>   3: TIP5P  TIP 5-point
> >>   4: SPCsimple point charge
> >>   5: SPC/E  extended simple point charge
> >>   6: None
> >> 6
> >> Opening force field file
> >> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.r2b
> >> Reading Ethylene.gro...
> >> Read 'Giant Rising Ordinary Mutants for A Clerical Setup', 6 atoms
> >> Analyzing pdb file
> >> Splitting PDB chains based on TER records or changing chain id.
> >> There are 1 chains and 0 blocks of water and 1 residues with 6 atoms
> >>
> >>chain  #res #atoms
> >>1 ' ' 1  6
> >>
> >> No occupancies in Ethylene.gro
> >> Opening force field file
> >> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomtypes.atp
> >> Atomtype 1
> >> Reading residue database... (oplsaa)
> >> Opening force field file
> >> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.rtp
> >> Residue 56
> >> Sorting it all out...
> >> Opening force field file
> >> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.hdb
> >> Opening force field file
> >> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.n.tdb
> >> Opening force field file
> >> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.c.tdb
> >>
> >> Back Off! I just backed up Ethylene.top to ./#Ethylene.top.1#
> >> Processing chain 1 (6 atoms, 1 residues)
> >> There are 0 donors and 0 acceptors
> >> There are 0 hydrogen bonds
> >> Warning: Starting residue ETY1 in chain not identified as
> Protein/RNA/DNA.
> >> Problem with chain definition, or missing terminal residues.
> >> This chain does not appear to contain a recognized chain molecule.
> >> If this is incorrect, you can edit residuetypes.dat to modify the
> >> behavior.
> >> 8 out of 8 lines of specbond.dat converted successfully
> >>
> >> --**-
> >> Program pdb2gmx, VERSION 4.5.4
> >> Source code file: resall.c, line: 581
> >>
> >> Fatal error:
> >> Residue 'ETY' not found in residue topology database
> >> For more information and tips for troubleshooting, please check the
> >> GROMACS
> >> website at http://www.gromacs.org/**Documentation/Errors<
> http://www.gromacs.org/Documentation/Errors>
> >>
> >>
> >> I am kind of baffled what could be wrong. I would really appreciate if
> you
> >> could comment on this. Is there a bug in pdb2gmx version 4.5.4 (which I
> >> doubt)?
> >> Do i have to edit esiduetypes.dat?
> >>
> >>
> > You've added the .rtp entry incorrectly.  pdb2gmx in version 4.5 and
> above
> > needs .rtp files to be organized in force field subdirectories (in your
> > case oplsaa.ff).  It will not recognize a file called "ffoplsa

Re: [gmx-users] amber99 with berger's lipids

[Mark Abraham]

How about reading the literature on combining AMBER and Berger? :-)

Mark

On Sat, Apr 6, 2013 at 8:24 AM, James Starlight wrote:

> Dear Gromacs Users!
>
>
> I'm looking for cut-offs parameters which would be suitable for the
> simulation of the membrane proteins (bergers united-atom lipids) with the
> amber-99 force fields (full-atomic protein representation). I'd be thankful
> to anyone who can provide me with such cut-offs for vdw as well as coulomb
> interactions for that force field.
>
>
>
> James
> --
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Re: [gmx-users] nstxout, nstvout, . . .

[Mark Abraham]

Only you can judge that, because only you know what you are trying to
observe.

Mark

On Sat, Apr 6, 2013 at 10:54 AM, dina dusti  wrote:

>
>
>
>
> 
>
> Dear Mark and Chandan kumar Choudhury
> Thank you very much from your answers. May I know what is the best of
> frequency to write the output (In MARTINI), Please?
> Best Regards
> Dina
>
>
>
>
> On Sat, Apr 6, 2013 at 8:25 AM, Chandan Choudhury 
> wrote:
>
> You need to re submit the jobs, with decreased time.
> >
>
> And next time check with the manual and consider your needs before making
> arbitrary choices :-)
>
> Mark
>
>
> >
> >--
> >Chandan kumar Choudhury
> >NCL, Pune
> >INDIA
> >
> >
> >
> >On Sat, Apr 6, 2013 at 11:20 AM, dina dusti  wrote:
> >
> >> Dear Specialists
> >>
> >>
> >> I am a beginner at Gromacs. I work with MARTINI CG force field.
> >>
> >> I selected 5 for
> >>
> >> nstxout= 5
> >> nstvout= 5
> >> nstenergy= 5
> >> nstlog= 5
> >> nstxtcout= 5
> >>
> >> and my jobs have been finished.
> >>
> >> I found that this time is very large. Is there a way for correct this
> >> time? Or, should I do these jobs again?!
> >> May I ask you to help me, Please?
> >> Best Regards
> >> Dina
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> * Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >--
> >gmx-users mailing listgmx-users@gromacs.org
> >http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
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Re: [gmx-users] RDF output has no data

[Mark Abraham]

On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy  wrote:

> There was no fatal error preceding the output. After selecting the groups
> following are the output on the screen
> Reading frame   1 time0.100
> Warning: can not make broken molecules whole without a run input file,
>  don't worry, mdrun doesn't write broken molecules
>

This message is from a prehistoric version of g_rdf. Please get a new one.

Mark


>
> Reading frame2000 time  200.000
>
>
> gcq#69: "The Wheels On the Bus Go Round and Round" (J. Richman)
>
> And the rdf.xvg file looks like this
>
> #This file was created Sat Apr  6 10:54:13 2013
> # by the following command:
> # g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg
> #
> # g_rdf is part of G R O M A C S:
> #
> # GROningen MAchine for Chemical Simulation
> #
> @title "Radial Distribution"
> @xaxis  label "r"
> @yaxis  label ""
> @TYPE xy
> @ subtitle "O21-H2_&_CAT"
>  0.001  1
> ~
>
> Whats going wrong? Please help.
>
>
> On Sat, Apr 6, 2013 at 12:41 AM, Justin Lemkul  wrote:
>
> > On Fri, Apr 5, 2013 at 2:30 PM, Venkat Reddy 
> wrote:
> >
> > > Dear users
> > >
> > > I have used AMBER MD package to run simulation for a solvent box. I am
> > now
> > > using the gromacs utility to calculate rdf as follows:
> > >
> > > g_rdf -f file.trr -s file.pdb -n rdf.ndx -o rdf.xvg
> > >
> > > However, I get no data in the output rdf.xvg. Since Im using specially
> > > generated force field parameters, I do not know how to go about
> > generating
> > > a tpr file (in case that is the problem). The rdf.ndx file is correct
> for
> > > my atom selection. Please suggest how to go about solving this.
> > >
> > >
> > Blank output usually indicates the command failed, which should have been
> > preceded by a rather obvious fatal error. If a .tpr file is required,
> g_rdf
> > will tell you (again, a fatal error).
> >
> > -Justin
> >
> > --
> >
> > 
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540)
> > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > 
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
>
>
>
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
> --
> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] nstxout, nstvout, . . .

[dina dusti]

Dear Mark and Chandan kumar Choudhury
Thank you very much from your answers. May I know what is the best of frequency 
to write the output (In MARTINI), Please?
Best Regards
Dina




On Sat, Apr 6, 2013 at 8:25 AM, Chandan Choudhury  wrote:

You need to re submit the jobs, with decreased time.
>

And next time check with the manual and consider your needs before making 
arbitrary choices :-)

Mark
 

>
>--
>Chandan kumar Choudhury
>NCL, Pune
>INDIA
>
>
>
>On Sat, Apr 6, 2013 at 11:20 AM, dina dusti  wrote:
>
>> Dear Specialists
>>
>>
>> I am a beginner at Gromacs. I work with MARTINI CG force field.
>>
>> I selected 5 for
>>
>> nstxout        = 5
>> nstvout        = 5
>> nstenergy    = 5
>> nstlog        = 5
>> nstxtcout                = 5
>>
>> and my jobs have been finished.
>>
>> I found that this time is very large. Is there a way for correct this
>> time? Or, should I do these jobs again?!
>> May I ask you to help me, Please?
>> Best Regards
>> Dina
>>
>> --
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>--
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Re: [gmx-users] nstxout, nstvout, . . .

[Mark Abraham]

On Sat, Apr 6, 2013 at 8:25 AM, Chandan Choudhury  wrote:

> You need to re submit the jobs, with decreased time.
>

And next time check with the manual and consider your needs before making
arbitrary choices :-)

Mark


>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Sat, Apr 6, 2013 at 11:20 AM, dina dusti  wrote:
>
> > Dear Specialists
> >
> >
> > I am a beginner at Gromacs. I work with MARTINI CG force field.
> >
> > I selected 5 for
> >
> > nstxout= 5
> > nstvout= 5
> > nstenergy= 5
> > nstlog= 5
> > nstxtcout= 5
> >
> > and my jobs have been finished.
> >
> > I found that this time is very large. Is there a way for correct this
> > time? Or, should I do these jobs again?!
> > May I ask you to help me, Please?
> > Best Regards
> > Dina
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
> --
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