Re: [gmx-users] increase the time frame

[Mark Abraham]

On 21/10/2011 5:09 PM, aiswarya pawar wrote:

Hi users,

Iam running a minimization on protein complex in vacuum. i have set 
the parameters as following-


; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment

title= Energy Minimization; Title of run

; The following line tell the program the standard locations where to 
find certain files

cpp= /lib/cpp; Preprocessor


; Define can be used to control processes
define  = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator= steepest; Algorithm (steep = steepest descent 
minimization)
emtol= 1000.0   ; Stop minimization when the maximum force 
< 1.0 kJ/mol

emstep  = 0.01
nsteps= 5; Maximum number of (minimization) steps 
to perform

nstenergy= 1  ; Write energies to disk every nstenergy steps
energygrps= Protein; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how 
to calculate the interactions

nstxout = 1
nstlist= 10; Frequency to update the neighbor list and 
long range forces
ns_type= grid  ; Method to determine neighbor list 
(simple, grid)
rlist= 1.0; Cut-off for making neighbor list (short 
range forces)
coulombtype= cutoff   ; Treatment of long range electrostatic 
interactions

rcoulomb= 1.0; long range electrostatic cut-off
rvdw= 1.4; long range Van der Waals cut-off
constraints= none; Bond types to replace by constraints
pbc= no; Periodic Boundary Conditions (yes/no)

But from this i could write only 2 frames i need to increase the time 
frames, what is to be changed in the parameters.


This will write every frame of the EM, but if it only has two steps...

Mark
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Re: [gmx-users] Re: Preparation of the pure lipid system with charmm force field

[Mark Abraham]

On 21/10/2011 5:41 PM, James Starlight wrote:
I've also tried to make topology for my system parametriesed for 
charmm36 ff by hands but failed too :(


This is my topology for the POPC bilayer wich I've made in VMD 
membrane builder as well as downloaded a pre built membrane system ( 
I've tested for both cases)


; Include chain topologies
#include "charmm36.ff/forcefield.itp"

; Include lipids
#include "charmm36.ff/lipids.rtp"


.rtp files may not be #included




; Include water topology
#include "/charmm36.ff/tip3p.itp"


Initial backslash refers to the root of your file system, so is likely 
wrong.




; Include ion topologies
#include "charmm36.ff/ions.itp"

; System specifications
[ system ]
128-Lipid POPC Bilayer in water

[ molecules ]
POPC 72

When I've loaded my molecule to grompp I've obtained error

Program grompp, VERSION 4.5.4
Source code file: /tmp/gromacs-4.5.4/src/kernel/toppush.c, line: 770

Fatal error:
Unknown bond_atomtype 1

What does it means? Is here anybody who also tried to parametriesed 
theis lipids by charmm ff ?


Don't blame the ff yet :-)

Mark
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[gmx-users] Re: Preparation of the pure lipid system with charmm force field

[James Starlight]

I've also tried to make topology for my system parametriesed for charmm36 ff
by hands but failed too :(

This is my topology for the POPC bilayer wich I've made in VMD membrane
builder as well as downloaded a pre built membrane system ( I've tested for
both cases)

; Include chain topologies
#include "charmm36.ff/forcefield.itp"

; Include lipids
#include "charmm36.ff/lipids.rtp"


; Include water topology
#include "/charmm36.ff/tip3p.itp"

; Include ion topologies
#include "charmm36.ff/ions.itp"

; System specifications
[ system ]
128-Lipid POPC Bilayer in water

[ molecules ]
POPC 72

When I've loaded my molecule to grompp I've obtained error

Program grompp, VERSION 4.5.4
Source code file: /tmp/gromacs-4.5.4/src/kernel/toppush.c, line: 770

Fatal error:
Unknown bond_atomtype 1

What does it means? Is here anybody who also tried to parametriesed theis
lipids by charmm ff ?


James

2011/10/20 James Starlight 

> Dear, Gromac's users!
>
>
> Today I've tried to make pure lipid bi-layer system from initial .pdb
> structure with the parametrization by the charmm ff. The main goal of this
> step is preparing the initial structure suitable for the futher simulation (
> creating gro, top and posre files)
>
> First I've download s system consisted of 72 dppc lipids solved with water.
> Then I've succesfull created .gro as well as .top files by the pdb2grmx for
> my lipid system.
> But on futher during creatinon of the tpr file by gromp I've obtained many
> errors like this
>
>
> ERROR 4378 [file topol.top, line 83773]:
>   No default U-B types
>
> Also I've tried to make my own bi-layer by VMD membrane plugin. After
> processing of this file by pdb2gmx I've obtained many .itp files like
> topol_Other_chain_L2.itp included in the generated topology file topol.top.
>
> But during loading this structure to the grompp I've obtained above
> mentioned error again. In both cases I've used mdp file for gromp consist of
> minimization algorithm ( attached).
>
> What I've done wrong? Could you provide me with the workable algorithm for
> preparation of the pure lipid system parametriezed by charm27 ?
>
>
> Finally I have small queation about charmm structures- I've found already
> pre-equilibrated bi-layers
> http://terpconnect.umd.edu/~jbklauda/research/download.html where each pdb
> file is accompanied by the PSF ones. As I've understood the PSF is the same
> to the top in the Gromacs. Could I convert PSF to the TOP for already
> pre-built system?
>
>
> Thanks for help
>
> James
>
> James
>
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Re: [gmx-users] extending simulation with grompp incorporating velocities

[Mark Abraham]

On 21/10/2011 4:51 PM, Chandan Choudhury wrote:
On Fri, Oct 21, 2011 at 10:26 AM, Mark Abraham 
mailto:mark.abra...@anu.edu.au>> wrote:


On 21/10/2011 3:25 PM, Chandan Choudhury wrote:


Dear gmx users,

A simulation was performed for 50 ns with

; RUN CONTROL
integrator   = md
nsteps   = 5000
dt   = 0.001
; OUTPUT CONTROL
nstxout  = 1000
nstvout  = 1000
nstxtcout= 0
nstlog   = 100
nstenergy= 100

The output produced were 0-50.edr, 0-50.trr, 0-50.log,
0-50.pdb state.cpt, state_prev.cpt. The simulation completed
normally.

After 50 ns, I intend to extend for 4 more ns, write the
trajectory file frequently with


Use tpbconv -extend. See
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations


I was aware with the tpbconv command. But while using the tpbconv 
command, we cannot change the output frequency. If somehow the 
trajectory writing frequency can be changed, it will solve my curiosity.


Ah. Well for a new .mdp, you need the combination of nsteps, init_step 
and the step number in the .cpt to all make mutual sense, and perhaps 
tinit, etc. also. gmxdump -cp may help here. Note that tinit and 
init_step refer to the whole simulation, not the start of any 
non-initial chunk.


Mark
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[gmx-users] increase the time frame

[aiswarya pawar]

Hi users,

Iam running a minimization on protein complex in vacuum. i have set the
parameters as following-

; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment

title= Energy Minimization; Title of run

; The following line tell the program the standard locations where to find
certain files
cpp= /lib/cpp; Preprocessor


; Define can be used to control processes
define  = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator= steepest; Algorithm (steep = steepest descent
minimization)
emtol= 1000.0   ; Stop minimization when the maximum force < 1.0
kJ/mol
emstep  = 0.01
nsteps= 5; Maximum number of (minimization) steps to
perform
nstenergy= 1  ; Write energies to disk every nstenergy steps
energygrps= Protein; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstxout = 1
nstlist= 10; Frequency to update the neighbor list and long
range forces
ns_type= grid  ; Method to determine neighbor list (simple,
grid)
rlist= 1.0; Cut-off for making neighbor list (short range
forces)
coulombtype= cutoff   ; Treatment of long range electrostatic
interactions
rcoulomb= 1.0; long range electrostatic cut-off
rvdw= 1.4; long range Van der Waals cut-off
constraints= none; Bond types to replace by constraints
pbc= no; Periodic Boundary Conditions (yes/no)

But from this i could write only 2 frames i need to increase the time
frames, what is to be changed in the parameters.

Thanks,
Aiswarya
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Re: [gmx-users] extending simulation with grompp incorporating velocities

[Chandan Choudhury]

On Fri, Oct 21, 2011 at 10:26 AM, Mark Abraham wrote:

> On 21/10/2011 3:25 PM, Chandan Choudhury wrote:
>
>>
>> Dear gmx users,
>>
>> A simulation was performed for 50 ns with
>>
>> ; RUN CONTROL
>> integrator   = md
>> nsteps   = 5000
>> dt   = 0.001
>> ; OUTPUT CONTROL
>> nstxout  = 1000
>> nstvout  = 1000
>> nstxtcout= 0
>> nstlog   = 100
>> nstenergy= 100
>>
>> The output produced were 0-50.edr, 0-50.trr, 0-50.log, 0-50.pdb state.cpt,
>> state_prev.cpt. The simulation completed normally.
>>
>> After 50 ns, I intend to extend for 4 more ns, write the trajectory file
>> frequently with
>>
>
> Use tpbconv -extend. See http://www.gromacs.org/**Documentation/How-tos/**
> Extending_Simulations


I was aware with the tpbconv command. But while using the tpbconv command,
we cannot change the output frequency. If somehow the trajectory writing
frequency can be changed, it will solve my curiosity.

Chandan



>
>
>  ; RUN CONTROL
>> integrator   = md
>> nsteps   = 400
>> dt   = 0.001
>> ; OUTPUT CONTROL
>> nstxout  = 00
>> nstvout  = 00
>> nstxtcout= 10
>> nstlog   = 500
>> nstenergy= 10
>>
>> $grompp -f md.mdp -p topol.top -o md50-54.tpr -c 0-50.pdb  -n index.ndx
>>
>> $gmxdump -s md50-54.tpr | more
>>
>> md50-54.tpr:
>> inputrec:
>>   integrator   = md
>>   nsteps   = 400
>>   init_step= 0
>>   ns_type  = Grid
>>   nstlist  = 10
>>   ndelta   = 2
>>   nstcomm  = 1
>>   comm_mode= Linear
>>   nstlog   = 500
>>   nstxout  = 0
>>   nstvout  = 0
>>   nstfout  = 0
>>   nstenergy= 10
>>   nstxtcout= 10
>>   init_t   = 0
>>   delta_t  = 0.001
>>   xtcprec  = 1000
>>   nkx  = 22
>>   nky  = 22
>>   nkz  = 40
>>   pme_order= 4
>>   ewald_rtol   = 1e-05
>>   ewald_geometry   = 0
>>   epsilon_surface  = 0
>>   optimize_fft = FALSE
>>   ePBC = xyz
>>   bPeriodicMols= FALSE
>>   bContinuation= FALSE
>>   bShakeSOR= FALSE
>>   etc  = V-rescale
>>   epc  = Berendsen
>>   epctype  = Isotropic
>>   tau_p= 1
>>
>> $mdrun_mpi-4.5.5 -s md50-54.tpr -c 50-54.pdb -x 50-54.xtc -e 50-54.edr -g
>> 50-54.log -cpi state.cpt -nice 0
>>
>> state.cpt is the output of the initial 50ns run. I have used state.cpt to
>> incorporate the velocities frm the initial run.
>> So, I would expect my 2nd simulation to get complete after running for 4
>> ns. But, that was not the case. I have checked the log file. The time
>> clearly exceeds 4ns.
>>
>> $ tail -15 50-54.log
>> DD  step 54500989 load imb.: force  5.6%  pme mesh/force 0.429
>>
>> DD  step 54500999 load imb.: force  6.0%  pme mesh/force 0.428
>>
>>   Step   Time Lambda
>>   5450100054501.002590.0
>>
>>   Energies (kJ/mol)
>>   Bond  AngleProper Dih. Ryckaert-Bell.  LJ-14
>>1.82780e+023.37147e+028.77788e+011.92877e+013.90071e+01
>> Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
>>5.96624e+027.91553e+04   -5.73437e+05   -2.73830e+04   -5.20402e+05
>>Kinetic En.   Total EnergyTemperature Pressure (bar)
>>9.75908e+04   -4.22811e+052.97855e+02   -5.82198e+01
>>
>> Kindly suggest what wrong am I doing. and how do I incorporate the
>> velocity from my earlier run.
>>
>
> On the information given, I can't explain this observation.
>
> Mark
> --
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> Please search the archive at http://www.gromacs.org/**
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Re: [gmx-users] extending simulation with grompp incorporating velocities

[Mark Abraham]

On 21/10/2011 3:25 PM, Chandan Choudhury wrote:


Dear gmx users,

A simulation was performed for 50 ns with

; RUN CONTROL
integrator   = md
nsteps   = 5000
dt   = 0.001
; OUTPUT CONTROL
nstxout  = 1000
nstvout  = 1000
nstxtcout= 0
nstlog   = 100
nstenergy= 100

The output produced were 0-50.edr, 0-50.trr, 0-50.log, 0-50.pdb 
state.cpt, state_prev.cpt. The simulation completed normally.


After 50 ns, I intend to extend for 4 more ns, write the trajectory 
file frequently with


Use tpbconv -extend. See 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations



; RUN CONTROL
integrator   = md
nsteps   = 400
dt   = 0.001
; OUTPUT CONTROL
nstxout  = 00
nstvout  = 00
nstxtcout= 10
nstlog   = 500
nstenergy= 10

$grompp -f md.mdp -p topol.top -o md50-54.tpr -c 0-50.pdb  -n index.ndx

$gmxdump -s md50-54.tpr | more

md50-54.tpr:
inputrec:
   integrator   = md
   nsteps   = 400
   init_step= 0
   ns_type  = Grid
   nstlist  = 10
   ndelta   = 2
   nstcomm  = 1
   comm_mode= Linear
   nstlog   = 500
   nstxout  = 0
   nstvout  = 0
   nstfout  = 0
   nstenergy= 10
   nstxtcout= 10
   init_t   = 0
   delta_t  = 0.001
   xtcprec  = 1000
   nkx  = 22
   nky  = 22
   nkz  = 40
   pme_order= 4
   ewald_rtol   = 1e-05
   ewald_geometry   = 0
   epsilon_surface  = 0
   optimize_fft = FALSE
   ePBC = xyz
   bPeriodicMols= FALSE
   bContinuation= FALSE
   bShakeSOR= FALSE
   etc  = V-rescale
   epc  = Berendsen
   epctype  = Isotropic
   tau_p= 1

$mdrun_mpi-4.5.5 -s md50-54.tpr -c 50-54.pdb -x 50-54.xtc -e 50-54.edr 
-g 50-54.log -cpi state.cpt -nice 0


state.cpt is the output of the initial 50ns run. I have used state.cpt 
to incorporate the velocities frm the initial run.
So, I would expect my 2nd simulation to get complete after running for 
4 ns. But, that was not the case. I have checked the log file. The 
time clearly exceeds 4ns.


$ tail -15 50-54.log
DD  step 54500989 load imb.: force  5.6%  pme mesh/force 0.429

DD  step 54500999 load imb.: force  6.0%  pme mesh/force 0.428

   Step   Time Lambda
   5450100054501.002590.0

   Energies (kJ/mol)
   Bond  AngleProper Dih. Ryckaert-Bell.  
LJ-14
1.82780e+023.37147e+028.77788e+011.92877e+01
3.90071e+01
 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  
Potential
5.96624e+027.91553e+04   -5.73437e+05   -2.73830e+04   
-5.20402e+05

Kinetic En.   Total EnergyTemperature Pressure (bar)
9.75908e+04   -4.22811e+052.97855e+02   -5.82198e+01

Kindly suggest what wrong am I doing. and how do I incorporate the 
velocity from my earlier run.


On the information given, I can't explain this observation.

Mark
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[gmx-users] extending simulation with grompp incorporating velocities

[Chandan Choudhury]

Dear gmx users,

A simulation was performed for 50 ns with

; RUN CONTROL
integrator   = md
nsteps   = 5000
dt   = 0.001
; OUTPUT CONTROL
nstxout  = 1000
nstvout  = 1000
nstxtcout= 0
nstlog   = 100
nstenergy= 100

The output produced were 0-50.edr, 0-50.trr, 0-50.log, 0-50.pdb state.cpt,
state_prev.cpt. The simulation completed normally.

After 50 ns, I intend to extend for 4 more ns, write the trajectory file
frequently with
; RUN CONTROL
integrator   = md
nsteps   = 400
dt   = 0.001
; OUTPUT CONTROL
nstxout  = 00
nstvout  = 00
nstxtcout= 10
nstlog   = 500
nstenergy= 10

$grompp -f md.mdp -p topol.top -o md50-54.tpr -c 0-50.pdb  -n index.ndx

$gmxdump -s md50-54.tpr | more

md50-54.tpr:
inputrec:
   integrator   = md
   nsteps   = 400
   init_step= 0
   ns_type  = Grid
   nstlist  = 10
   ndelta   = 2
   nstcomm  = 1
   comm_mode= Linear
   nstlog   = 500
   nstxout  = 0
   nstvout  = 0
   nstfout  = 0
   nstenergy= 10
   nstxtcout= 10
   init_t   = 0
   delta_t  = 0.001
   xtcprec  = 1000
   nkx  = 22
   nky  = 22
   nkz  = 40
   pme_order= 4
   ewald_rtol   = 1e-05
   ewald_geometry   = 0
   epsilon_surface  = 0
   optimize_fft = FALSE
   ePBC = xyz
   bPeriodicMols= FALSE
   bContinuation= FALSE
   bShakeSOR= FALSE
   etc  = V-rescale
   epc  = Berendsen
   epctype  = Isotropic
   tau_p= 1

$mdrun_mpi-4.5.5 -s md50-54.tpr -c 50-54.pdb -x 50-54.xtc -e 50-54.edr -g
50-54.log -cpi state.cpt -nice 0

state.cpt is the output of the initial 50ns run. I have used state.cpt to
incorporate the velocities frm the initial run.
So, I would expect my 2nd simulation to get complete after running for 4 ns.
But, that was not the case. I have checked the log file. The time clearly
exceeds 4ns.

$ tail -15 50-54.log
DD  step 54500989 load imb.: force  5.6%  pme mesh/force 0.429

DD  step 54500999 load imb.: force  6.0%  pme mesh/force 0.428

   Step   Time Lambda
   5450100054501.002590.0

   Energies (kJ/mol)
   Bond  AngleProper Dih. Ryckaert-Bell.  LJ-14
1.82780e+023.37147e+028.77788e+011.92877e+013.90071e+01
 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
5.96624e+027.91553e+04   -5.73437e+05   -2.73830e+04   -5.20402e+05
Kinetic En.   Total EnergyTemperature Pressure (bar)
9.75908e+04   -4.22811e+052.97855e+02   -5.82198e+01

Kindly suggest what wrong am I doing. and how do I incorporate the velocity
from my earlier run.

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA
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Re: [gmx-users] gromacs command help text

[Sikandar Mashayak]

Hey Justin,

-quiet works

thanks

---
sikandar

On Thu, Oct 20, 2011 at 10:22 AM, Justin A. Lemkul  wrote:

>
>
> Sikandar Mashayak wrote:
>
>> Hi
>>
>> All gromacs commands print the help text every time they are run. Is there
>> a way to tell gromacs command not to print help text?
>>
>>
> Use the -quiet option.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
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Re: [gmx-users] Re: Re: Reference structure for g_covar

[Tsjerk Wassenaar]

Hi Vivek,

The high cosine content of the first pc indicates that the system is still
equilibrating. You're sort of still on the road from A (the starting
position) to B (the equilibrated state).

Hope it helps,

Tsjerk

On Oct 20, 2011 5:07 PM, "vivek modi"  wrote:

Hi Tsjerk,

Thanks a lot for your reply.
But now I will ask a very naive  question.

My study involves understanding the dynamics of a group of closely related
proteins. All of them are simulated for a period of 100ns each.
I have also analyzed the RMSD using g_rms for all of them and it  becomes
very stable after 20-30ns for all the proteins.
But when I do PCA I see high cosines (~0.8) for the first PC. For all the
other PCs the cosine content is very low.

The question is  that is it appropriate to ignore the first PC and make
inference about the motion of the protein by using other PCs ?


Thanks a lot.


Regards,

-Vivek Modi

Date: Wed, 19 Oct 2011 13:58:00 +0200
> From: Tsjerk Wassenaar 
> Subject: Re: [gmx-users] Reference structure for g_covar
> To: Discussion list for GROMACS users 
> Message-ID:
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> > > Hi Vivek, > > I explained related matters in some detail on this list
> earlier, and > would urge...
>


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Re: [gmx-users] gromacs command help text

[Justin A. Lemkul]

Sikandar Mashayak wrote:

Hi

All gromacs commands print the help text every time they are run. Is 
there a way to tell gromacs command not to print help text?




Use the -quiet option.

-Justin

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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: Re: Reference structure for g_covar

[vivek modi]

Hi Tsjerk,

Thanks a lot for your reply.
But now I will ask a very naive  question.

My study involves understanding the dynamics of a group of closely related
proteins. All of them are simulated for a period of 100ns each.
I have also analyzed the RMSD using g_rms for all of them and it  becomes
very stable after 20-30ns for all the proteins.
But when I do PCA I see high cosines (~0.8) for the first PC. For all the
other PCs the cosine content is very low.

The question is  that is it appropriate to ignore the first PC and make
inference about the motion of the protein by using other PCs ?


Thanks a lot.


Regards,

-Vivek Modi

Date: Wed, 19 Oct 2011 13:58:00 +0200
> From: Tsjerk Wassenaar 
> Subject: Re: [gmx-users] Reference structure for g_covar
> To: Discussion list for GROMACS users 
> Message-ID:
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Vivek,
>
> I explained related matters in some detail on this list earlier, and
> would urge not to use a structure other than the average for
> determining the components.
>
> The results on the cosine contents can be illustrated as follows:
>
> I. Using average
>
> Imagine you're moving from place A to place B. The principal component
> is B-A, and the average is (A+B)/2. Your score/projection is the
> position relative to the average; negative on one side, positive on
> the other. This ends up being a straight line in one dimension, but in
> higher dimensions you'll get a nice half cosine.
>
> II. Using fixed reference
>
> Let's say your reference is A, then your component is still B-A, but
> your score/projection is now the distance from A. It starts out at
> zero and increases. In higher dimensional space, this would give a
> projection that starts out approximately linear and levels off at some
> point. These components are awkward, and very hard to interpret.
>
> Hope it helps,
>
> Tsjerk
>
>
> On Wed, Oct 19, 2011 at 10:08 AM, vivek modi 
> wrote:
> > Hi,
> >
> > I am doing Essential Dynamics on a protein (150 residues). The simulation
> is
> > 100ns long and the RMSD becomes very stable after 25ns.
> > I have gone through the mailing list archives but could not find a
> precise
> > answer to the following question.
> >
> > When I calculate the cosine content for the first PC by taking the
> average
> > structure for fitting using g_covar it gives a very high value ~.8.
> > But when I change the reference structure to the starting structure then
> I
> > get a cosine value ~.1.
> >
> > I also repeated the same by dividing my trajectory into two equal halves
> but
> > the cosine value with average structure as a reference is always very
> high
> > while it is reasonably low with starting structure taken as reference.
> >
> > My question is why the cosine content is dependent on the fitting
> > structure used in g_covar?  And, especially, which structure is
> > recommended to use in Essential Dynamics analysis ?
> >
> >
> > Any help is appreciated.
> >
> >
> > Thanks a lot.
> >
> >
> > Regards,
> >
> > Vivek Modi
> > Graduate Student,
> > IITK.
> >
> > --
> > 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
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>
>
>
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[gmx-users] gromacs command help text

[Sikandar Mashayak]

Hi

All gromacs commands print the help text every time they are run. Is there a
way to tell gromacs command not to print help text?

thanks
sikandar
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Re: [gmx-users] potential energy of one molecule using GAFF: confused regarding Ryckaert-Bellemans and 1-4 potentials

[Vedat Durmaz]

Am 20.10.2011 15:01, schrieb Mark Abraham:

On 20/10/2011 7:25 PM, Vedat Durmaz wrote:


thanks mark. i guess it took some time answering all these questions. 
and i think you are right. trying to interpret each computed energy 
term seperately in a physical manner is senseless. especially since 
i'm not really deep inside the force field & implementation stuff. 
however, with one of your statements i cannot agree at all:


imho, free energy diff's on the basis of two conformations and their 
steady state distribution are independent from both the energy and 
type of the intermediate state. it's only the conversion's rate that 
does depend on it.


I'm not sure with which statement of mine you are disagreeing. 


actually with this one: "Measuring the free energy difference with 
simulations is hard because you cannot model the intermediate stages of 
bond breaking and forming."


The free energy is a state function, and so the free energy difference 
between E and Z isomers does not depend on the path taken for the 
conversion. The difficulty is just that there is no path for a cyclic 
alkane from E to Z in a normal MD force field.
and that's the reason for the disagreement. also imho, the path is 
irrelevant. for a molecule given with a cis and a trans configuration, 
respectively (same atoms, quasi-same topology), the inner energy and 
entropy of both conformations (derived from classical force field 
simulations) is enough in order to get the free energy difference.




but the reason, why i refrained from extracting the potential energy 
for a subset of my system was simply due to the difficulties to find 
"detailed information" about how to play it out although many gromacs 
users have been asking for the issue over the last years. i needed 
nearly one full day to figure it out even though it's a simple series 
of about 4 gromacs commands only, given some md input & result files 
like md.xtc, md.gro, complex.top, index.ndx:


|grompp -f mdSubset.mdp -c md.gro -p complex.top -o mdSubsetTemp.tpr|
|echo ||"1"| || tpbconv -s mdSubsetTemp.tpr -nsteps ||0| |-n 
index.ndx -o mdSubset.tpr|

|echo ||"1"| || trjconv -s mdSubset.tpr -f md.xtc -o mdSubset.xtc|
|mdrun -s mdSubset.tpr -rerun mdSubset.xtc -v -deffnm mdSubset|

where "1" stands for the group to be extracted (from the list of 
groups in the index file) and "-nsteps 0" causes recomputation of for 
the extracted subset at the given time steps only. i mention it here 
so that other users looking for the details might find them a little 
bit faster ... it's especially this kind of "tiny tutorials" that i 
miss e. g. on the gromacs website.


There's an art to trying to find detailed help. I know I've given the 
advice to make subsets and use mdrun -rerun several times, but I don't 
know how a newcomer is ever going to figure that out on their own!
Your somehow right, but unfortunately, i'm no artist at all. However, 
what's the reason for the availability of all the tutorials and how-tos 
on the gromacs documentation site? i'll tell you: it helps other 
researchers to reduce times of searching/finding/figuring out. and 
besides, the information retrieved from the tools' manpage or the manual 
is often far away from being helpful!


please, don't misunderstand me. i'm just saying: if there are how-tos 
about how to plot data, perform calculations of pKa values or diffusion 
constants, then the description of getting the potEnergy of one of the 
systems components has an a fortiori right to exist there or somewhere 
else at a central place within the gromacs world!




BTW -nsteps 0 is not necessary. mdrun -rerun only computes on the 
frames present in the input trajectory file. Also, if the index group 
of interest is already present in the .tpr that ran the simulation, 
then you can do the job with variations on only the latter three commands.


thanks for the hints!



Mark


vedat



ps: don't kill me now ...




thanks for listening and kind regards,

vedat






Q8 does anyone have an idea, how to perform the simulation and on 
which energy terms to concentrate in order to get reliable results?


You seem to be performing it OK, given that you've said very little 
about any details...


I think the problem is poorly constructed. You have some 
experimental data that gives a general understanding of the size of 
the free energy difference between the isomers. You can't 
necessarily expect to reproduce that from (average) potential energy 
differences between conformations of those isomers. Measuring the 
free energy difference with simulations is hard because you cannot 
model the intermediate stages of bond breaking and forming. There 
are "alchemical" free energy methods that could in principle treat 
this problem effectively, but there will be some significant issues 
and you are best doing your own homework there.


Mark





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Re: [gmx-users] potential energy of one molecule using GAFF: confused regarding Ryckaert-Bellemans and 1-4 potentials

[Mark Abraham]

On 20/10/2011 7:25 PM, Vedat Durmaz wrote:


thanks mark. i guess it took some time answering all these questions. 
and i think you are right. trying to interpret each computed energy 
term seperately in a physical manner is senseless. especially since 
i'm not really deep inside the force field & implementation stuff. 
however, with one of your statements i cannot agree at all:


imho, free energy diff's on the basis of two conformations and their 
steady state distribution are independent from both the energy and 
type of the intermediate state. it's only the conversion's rate that 
does depend on it.


I'm not sure with which statement of mine you are disagreeing. The free 
energy is a state function, and so the free energy difference between E 
and Z isomers does not depend on the path taken for the conversion. The 
difficulty is just that there is no path for a cyclic alkane from E to Z 
in a normal MD force field.




but the reason, why i refrained from extracting the potential energy 
for a subset of my system was simply due to the difficulties to find 
"detailed information" about how to play it out although many gromacs 
users have been asking for the issue over the last years. i needed 
nearly one full day to figure it out even though it's a simple series 
of about 4 gromacs commands only, given some md input & result files 
like md.xtc, md.gro, complex.top, index.ndx:


|grompp -f mdSubset.mdp -c md.gro -p complex.top -o mdSubsetTemp.tpr|
|echo ||"1"| || tpbconv -s mdSubsetTemp.tpr -nsteps ||0| |-n index.ndx 
-o mdSubset.tpr|

|echo ||"1"| || trjconv -s mdSubset.tpr -f md.xtc -o mdSubset.xtc|
|mdrun -s mdSubset.tpr -rerun mdSubset.xtc -v -deffnm mdSubset|

where "1" stands for the group to be extracted (from the list of 
groups in the index file) and "-nsteps 0" causes recomputation of for 
the extracted subset at the given time steps only. i mention it here 
so that other users looking for the details might find them a little 
bit faster ... it's especially this kind of "tiny tutorials" that i 
miss e. g. on the gromacs website.


There's an art to trying to find detailed help. I know I've given the 
advice to make subsets and use mdrun -rerun several times, but I don't 
know how a newcomer is ever going to figure that out on their own!


BTW -nsteps 0 is not necessary. mdrun -rerun only computes on the frames 
present in the input trajectory file. Also, if the index group of 
interest is already present in the .tpr that ran the simulation, then 
you can do the job with variations on only the latter three commands.


Mark



thanks for listening and kind regards,

vedat






Q8 does anyone have an idea, how to perform the simulation and on 
which energy terms to concentrate in order to get reliable results?


You seem to be performing it OK, given that you've said very little 
about any details...


I think the problem is poorly constructed. You have some experimental 
data that gives a general understanding of the size of the free 
energy difference between the isomers. You can't necessarily expect 
to reproduce that from (average) potential energy differences between 
conformations of those isomers. Measuring the free energy difference 
with simulations is hard because you cannot model the intermediate 
stages of bond breaking and forming. There are "alchemical" free 
energy methods that could in principle treat this problem 
effectively, but there will be some significant issues and you are 
best doing your own homework there.


Mark





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[gmx-users] Preparation of the pure lipid system with charmm force field

[James Starlight]

Dear, Gromac's users!


Today I've tried to make pure lipid bi-layer system from initial .pdb
structure with the parametrization by the charmm ff. The main goal of this
step is preparing the initial structure suitable for the futher simulation (
creating gro, top and posre files)

First I've download s system consisted of 72 dppc lipids solved with water.
Then I've succesfull created .gro as well as .top files by the pdb2grmx for
my lipid system.
But on futher during creatinon of the tpr file by gromp I've obtained many
errors like this


ERROR 4378 [file topol.top, line 83773]:
  No default U-B types

Also I've tried to make my own bi-layer by VMD membrane plugin. After
processing of this file by pdb2gmx I've obtained many .itp files like
topol_Other_chain_L2.itp included in the generated topology file topol.top.

But during loading this structure to the grompp I've obtained above
mentioned error again. In both cases I've used mdp file for gromp consist of
minimization algorithm ( attached).

What I've done wrong? Could you provide me with the workable algorithm for
preparation of the pure lipid system parametriezed by charm27 ?


Finally I have small queation about charmm structures- I've found already
pre-equilibrated bi-layers
http://terpconnect.umd.edu/~jbklauda/research/download.html where each pdb
file is accompanied by the PSF ones. As I've understood the PSF is the same
to the top in the Gromacs. Could I convert PSF to the TOP for already
pre-built system?


Thanks for help

James
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Re: [gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:

Justin,

2011/10/19 Justin A. Lemkul mailto:jalem...@vt.edu>>


It won't cause errors, per se, but it does indicate that your system
is not equilibrated (nor should you expect it to be after only 1
ns).  After 20 ns or so of equilibration, most membrane systems
should be devoid of internal water and should be well-equilibrated.


It's crear now. At the current stage I've being tried 20ns equilibration 
of my same system prepared by G_membed so I hope that I'll get better 
results in this case :)
 



You'll never get a good comparison.


I've tried to analysy my system via your GridMAt software  as well as by 
the GROMACSs functions.


First of all my system was very stable- the RMSD deviation < 1A and 
small Rg indicate on the stability of the protein within the membrane as 
well.


Also I've obtain S per lipid by GridMat of 68 A^2 that is good result. 
Finally, I've analyzed Lateral Diffusion of Lipids- this value vas up to 
0.1 nm during 1ns stimulation as well as density for lipids groups ( 
this was near 200 kg m^-3 for both groups ). What values for two last 
measurements are normal for such system as KALP in DPPC?





Please search the literature.  I don't know what these values should be offhand. 
 I don't know if anyone has made such measurements.




Finally I wounder to simulate pure lipid bi layer with different force 
fields ( e.g I want to test Charmm ff). Could I use the md parametries 
from the KALP simulation for the pure bi-layer ? What are main 
differences beetween simulation of the pure bilayer and system with the 
protein?




Different force fields require different settings, most notably cutoffs. 
Understanding the intrinsics of the chosen force field is a prerequisite for 
using it.  Again, time spent in the literature here is more valuable than me 
spitting out settings that you should use.  You'll learn far more by discovering 
it yourself.


-Justin

--


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


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Re: [gmx-users] second defaults directive

[Justin A. Lemkul]

madhumita das wrote:

Hi Gromacs Users,
 
I have created a .gro file and topology file using acpype.py of a 
membrane protein. At the time of lipid shrinking when I go to generate 
.tpr file following error comes.

 Fatal error:
  Syntax error - File topol.top, line 8
  Last line read:
'  11   no  1.0 1.0'
   Found a second defaults directive.



http://www.gromacs.org/Documentation/Errors#Found_a_second_defaults_directive_file

-Justin

--


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


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[gmx-users] Preparation of the pure lipid system with charmm force field

[James Starlight]

Dear, Gromac's users!


Today I've tried to make pure lipid bi-layer system from initial .pdb
structure with the parametrization by the charmm ff. The main goal of this
step is preparing the initial structure suitable for the futher simulation (
creating gro, top and posre files)

First I've download s system consisted of 72 dppc lipids solved with water.
Then I've succesfull created .gro as well as .top files by the pdb2grmx for
my lipid system.
But on futher during creatinon of the tpr file by gromp I've obtained many
errors like this


ERROR 4378 [file topol.top, line 83773]:
  No default U-B types

Also I've tried to make my own bi-layer by VMD membrane plugin. After
processing of this file by pdb2gmx I've obtained many .itp files like
topol_Other_chain_L2.itp included in the generated topology file topol.top.

But during loading this structure to the grompp I've obtained above
mentioned error again. In both cases I've used mdp file for gromp consist of
minimization algorithm ( attached).

What I've done wrong? Could you provide me with the workable algorithm for
preparation of the pure lipid system parametriezed by charm27 ?


Finally I have small queation about charmm structures- I've found already
pre-equilibrated bi-layers
http://terpconnect.umd.edu/~jbklauda/research/download.html where each pdb
file is accompanied by the PSF ones. As I've understood the PSF is the same
to the top in the Gromacs. Could I convert PSF to the TOP for already
pre-built system?


Thanks for help

James

James


topol.top
Description: Binary data


minim.mdp
Description: application/mdp
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[gmx-users] force field for argon

[Dmitri Dubov]

Dear gmx'ers,

Inspecting gromacs' OPLSAA files, I find here two atom types for argon. File 
ffoplsaa.atp includes:
 opls_097   39.94800  ; Argon from Verlet & Weis Mol.Phys.,24,1013 (1972) 
and
 Ar 39.948; Argon

LJ parameters are (file ffoplsaanb.itp):
[ atomtypes ]
; name  bond_typemasscharge   ptype  sigma  epsilon
 opls_097   Ar  18   39.94800 0.000   A3.40100e-01  9.78638e-01 ; 
SIG
...
 Ar Ar 18   39.94800 0.000   A3.41000e-01  2.74580e-02

The first set looks somewhat like the real Ar--Ar pair potential. 
A short comment before the second set says:
; These ion atomtypes are NOT part of OPLS, but since they are
; needed for some proteins or tutorial Argon simulations we have added them.

But its well depth is extremely low! What simulations is this set intended for?
-- 
Regards,
 Dmitri  mailto:ddu...@ngs.ru-- 
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[gmx-users] second defaults directive

[madhumita das]

Hi Gromacs Users,

I have created a .gro file and topology file using acpype.py of a membrane
protein. At the time of lipid shrinking when I go to generate .tpr file
following error comes.
 Fatal error:
  Syntax error - File topol.top, line 8
  Last line read:
'  11   no  1.0 1.0'
   Found a second defaults directive.
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Re: [gmx-users] potential energy of one molecule using GAFF: confused regarding Ryckaert-Bellemans and 1-4 potentials

[Vedat Durmaz]

thanks mark. i guess it took some time answering all these questions. 
and i think you are right. trying to interpret each computed energy term 
seperately in a physical manner is senseless. especially since i'm not 
really deep inside the force field & implementation stuff. however, with 
one of your statements i cannot agree at all:


imho, free energy diff's on the basis of two conformations and their 
steady state distribution are independent from both the energy and type 
of the intermediate state. it's only the conversion's rate that does 
depend on it.


but the reason, why i refrained from extracting the potential energy for 
a subset of my system was simply due to the difficulties to find 
"detailed information" about how to play it out although many gromacs 
users have been asking for the issue over the last years. i needed 
nearly one full day to figure it out even though it's a simple series of 
about 4 gromacs commands only, given some md input & result files like 
md.xtc, md.gro, complex.top, index.ndx:


|grompp -f mdSubset.mdp -c md.gro -p complex.top -o mdSubsetTemp.tpr|
|echo ||"1"| || tpbconv -s mdSubsetTemp.tpr -nsteps ||0| |-n index.ndx 
-o mdSubset.tpr|

|echo ||"1"| || trjconv -s mdSubset.tpr -f md.xtc -o mdSubset.xtc|
|mdrun -s mdSubset.tpr -rerun mdSubset.xtc -v -deffnm mdSubset|

where "1" stands for the group to be extracted (from the list of groups 
in the index file) and "-nsteps 0" causes recomputation of for the 
extracted subset at the given time steps only. i mention it here so that 
other users looking for the details might find them a little bit faster 
... it's especially this kind of "tiny tutorials" that i miss e. g. on 
the gromacs website.


thanks for listening and kind regards,

vedat






Q8 does anyone have an idea, how to perform the simulation and on 
which energy terms to concentrate in order to get reliable results?


You seem to be performing it OK, given that you've said very little 
about any details...


I think the problem is poorly constructed. You have some experimental 
data that gives a general understanding of the size of the free energy 
difference between the isomers. You can't necessarily expect to 
reproduce that from (average) potential energy differences between 
conformations of those isomers. Measuring the free energy difference 
with simulations is hard because you cannot model the intermediate 
stages of bond breaking and forming. There are "alchemical" free 
energy methods that could in principle treat this problem effectively, 
but there will be some significant issues and you are best doing your 
own homework there.


Mark
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Re: [gmx-users] Solvent accessible surface area units

[Mark Abraham]

On 20/10/2011 4:51 PM, Sai Pooja wrote:

Hi,

It is not clear what are the units of SAS from g_SAS. The output gives
the units -  xaxis  label "Time (ps)"
@yaxis  label "Area (nm\S2\N)".

I would really appreciate it if someone could elaborate on (nm/S2/N).

Thanks and regards,

Pooja


See http://www.gromacs.org/Documentation/How-tos/Graphing_Data

Mark
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Re: [gmx-users] Simulation of membrane protein

[James Starlight]

Justin,

2011/10/19 Justin A. Lemkul 

>
>  It won't cause errors, per se, but it does indicate that your system is
> not equilibrated (nor should you expect it to be after only 1 ns).  After 20
> ns or so of equilibration, most membrane systems should be devoid of
> internal water and should be well-equilibrated.


It's crear now. At the current stage I've being tried 20ns equilibration of
my same system prepared by G_membed so I hope that I'll get better results
in this case :)


>
> You'll never get a good comparison.
>

I've tried to analysy my system via your GridMAt software  as well as by the
GROMACSs functions.

First of all my system was very stable- the RMSD deviation < 1A and small Rg
indicate on the stability of the protein within the membrane as well.

Also I've obtain S per lipid by GridMat of 68 A^2 that is good result.
Finally, I've analyzed Lateral Diffusion of Lipids- this value vas up to 0.1
nm during 1ns stimulation as well as density for lipids groups ( this was
near 200 kg m^-3 for both groups ). What values for two last measurements
are normal for such system as KALP in DPPC?



Finally I wounder to simulate pure lipid bi layer with different force
fields ( e.g I want to test Charmm ff). Could I use the md parametries from
the KALP simulation for the pure bi-layer ? What are main differences
beetween simulation of the pure bilayer and system with the protein?


James
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