[gmx-users] beta peptide parameters

[Michael McGovern]

Hello everyone.

I'm trying to do a simulation involving beta peptides.  There have been several 
papers published where parameters were developed and used.  I've tried multiple 
times to contact the authors to get more specifics on the parameters they used, 
but I haven't gotten a reply.  Does anyone know where else I might be able to 
turn to get these parameters?

Thanks a lot for your time.


  
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Re: [gmx-users] input the .gro and .trr file to the VMD

[Dallas B. Warren]

Best idea is to ask the vmd people, they have their own emailing list.

Catch ya,
Dallas Warren

A polar bear is a Cartesian bear that has undergone a polar  
transformation


On 28/04/2009, at 12:29 PM, "He, Yang"  wrote:


HI Mark,

I am indeed using the coarse-graining atoms .What do you mean by "  
tell
VMD to use suitable rules, or something similar." Do you have any  
fixed case about how to solve this problem in vmd?


Thank you very much.

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org]  
On Behalf Of Mark Abraham [mark.abra...@anu.edu.au]

Sent: Monday, April 27, 2009 7:00 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] input the .gro and .trr file to the VMD

He, Yang wrote:

Hi all users,

I want to get some snap shots from VMD through inputing my gro and  
trr file to  the VMD. But I always find that I can not get the bond  
connection among the atoms and then, I try to use the dynamic bonds  
to solve this problem but  another problem is that  when I define a  
value for the cutoff distance, the bonds which don't exist among  
the atoms in the original shape will also come up .


VMD guess at bonds based on atom names and inter-atomic distances, so
your .gro file isn't following the rules it expects. Either your
structures are broken, or they're coarse-grained and you need to tell
VMD to use suitable rules, or something similar.

Mark

Except the dynamic method to figure out this problem, I wonder  
whether there are other ways to fix this problem.


Thank you for any suggestions.

Yang
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RE: [gmx-users] input the .gro and .trr file to the VMD

[He, Yang]

HI Mark,

I am indeed using the coarse-graining atoms .What do you mean by " tell
VMD to use suitable rules, or something similar." Do you have any fixed case 
about how to solve this problem in vmd?

Thank you very much.

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Monday, April 27, 2009 7:00 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] input the .gro and .trr file to the VMD

He, Yang wrote:
> Hi all users,
>
> I want to get some snap shots from VMD through inputing my gro and trr file 
> to  the VMD. But I always find that I can not get the bond connection among 
> the atoms and then, I try to use the dynamic bonds to solve this problem but  
> another problem is that  when I define a value for the cutoff distance, the 
> bonds which don't exist among the atoms in the original shape will also come 
> up .

VMD guess at bonds based on atom names and inter-atomic distances, so
your .gro file isn't following the rules it expects. Either your
structures are broken, or they're coarse-grained and you need to tell
VMD to use suitable rules, or something similar.

Mark

> Except the dynamic method to figure out this problem, I wonder whether there 
> are other ways to fix this problem.
>
> Thank you for any suggestions.
>
> Yang
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Re: [gmx-users] input the .gro and .trr file to the VMD

[Mark Abraham]

He, Yang wrote:

Hi all users,

I want to get some snap shots from VMD through inputing my gro and trr file to  
the VMD. But I always find that I can not get the bond connection among the 
atoms and then, I try to use the dynamic bonds to solve this problem but  
another problem is that  when I define a value for the cutoff distance, the 
bonds which don't exist among the atoms in the original shape will also come up 
.


VMD guess at bonds based on atom names and inter-atomic distances, so 
your .gro file isn't following the rules it expects. Either your 
structures are broken, or they're coarse-grained and you need to tell 
VMD to use suitable rules, or something similar.


Mark


Except the dynamic method to figure out this problem, I wonder whether there 
are other ways to fix this problem.

Thank you for any suggestions.

Yang
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Re: [gmx-users] Identical energies generated in a rerun calculation ... but ...

[Mark Abraham]

David van der Spoel wrote:

Justin A. Lemkul wrote:


Hi Mark,

I tried applying your patch and found some odd installation behavior.  
We have two systems that I am trying to patch.  The first uses gcc-3.3 
and worked fine.  The other uses gcc-4.2.2, and the compilation failed 
with:


"md.c", line 933.18: 1506-046 (S) Syntax error.
"md.c", line 934.11: 1506-277 (S) Syntax error: possible missing ';' 
or ','?

make[3]: *** [md.o] Error 1
make[3]: Leaving directory `/home/rdiv1001/gmx/gromacs-4.0.4/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/rdiv1001/gmx/gromacs-4.0.4/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/rdiv1001/gmx/gromacs-4.0.4/src'
make: *** [all-recursive] Error 1

The error seems to point to this line:

 } else { // DDMASTER(cr->dd) == TRUE

Is the statement at the end supposed to be a comment?  I'm only a 
novice at C, so I'm used to seeing something more like:


 } else { /* DDMASTER(cr->dd) == TRUE */

If I make that change, then the system using gcc-4.2.2 doesn't 
complain and the installation finishes successfully.  I don't want to 
go haphazardly commenting out lines of code, so I'd appreciate any 
feedback on what might be going on.


// style comments are C++ only. They are not allowed in GROMACS for this 
reason.


Ah yes. My bad.

Mark
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[gmx-users] input the .gro and .trr file to the VMD

[He, Yang]

Hi all users,

I want to get some snap shots from VMD through inputing my gro and trr file to  
the VMD. But I always find that I can not get the bond connection among the 
atoms and then, I try to use the dynamic bonds to solve this problem but  
another problem is that  when I define a value for the cutoff distance, the 
bonds which don't exist among the atoms in the original shape will also come up 
.

Except the dynamic method to figure out this problem, I wonder whether there 
are other ways to fix this problem.

Thank you for any suggestions.

Yang
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Re: [gmx-users] Resizing membrane (dopc, berger)

[shayamra]

Hi Chris,

Thanks a lot for your quick reply - I will try to equilibrate.
-Shay

Quoting chris.ne...@utoronto.ca:

The simplest way to get around what you describe is to continue with  
your procedure and then equilibrate your membrane. Use semiisotropic  
pressure coupling and you will have what you want after 20-50 ns.  
You could alternatively build and equilibrate your own membrane, but  
this will require approximately the same amount of simulation time.


I wouldn't be surprised if you can fix this problem as a side-effect  
of the inflategro script. You could also use the make-hole version  
of gromacs 3.1.4 to keep your waters from entering the membrane  
during equilibration. However, you should be easily able to  
equilibrate your membrane within one week of wall time so the  
brute-force method may be faster for you than learning some new tools.


Chris.

-- original message --

Hello dear GROMACS users,

Lately I have been trying to user dopc membrane, using Berger united
atoms and I am confounded by a problem regarding the size of the
membrane.
The original membrane from the website is X Y Z (including 128
lipids). Now I would like to multiply the membrane by 1.5 and I cannot
find how.
Is there a (relatively) simple way of doing it?
I have tried several approaches:
1) genconf -f dopc128.gro -o dopc_new.gro -nbox 2 2 1
This option can only multiply the by *whole* integer numbers.

2) genconf -f dopc128.gro -o dopc_new.gro -box 1.5X 1.5Y Z # (X and Y
multiplied by 1.5, Z is unchanged).
The dopc_new.gro file will contain X1.5 molecules, but the water
molecules will extend much further than the lipid molecules. So now
there's a small "vacuum" in the gap between upper/lower leaflets of
the membrane in which water can invade.

I would much like to be able to use X1.5 and not X2 since that would
"save" me a whole lot of water/other molecules in the Z-axis, and
therefore simulation time too.

Thanks in advance,
-Shay

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[gmx-users] Resizing membrane (dopc, berger)

[chris . neale]

The simplest way to get around what you describe is to continue with  
your procedure and then equilibrate your membrane. Use semiisotropic  
pressure coupling and you will have what you want after 20-50 ns. You  
could alternatively build and equilibrate your own membrane, but this  
will require approximately the same amount of simulation time.


I wouldn't be surprised if you can fix this problem as a side-effect  
of the inflategro script. You could also use the make-hole version of  
gromacs 3.1.4 to keep your waters from entering the membrane during  
equilibration. However, you should be easily able to equilibrate your  
membrane within one week of wall time so the brute-force method may be  
faster for you than learning some new tools.


Chris.

-- original message --

Hello dear GROMACS users,

Lately I have been trying to user dopc membrane, using Berger united
atoms and I am confounded by a problem regarding the size of the
membrane.
The original membrane from the website is X Y Z (including 128
lipids). Now I would like to multiply the membrane by 1.5 and I cannot
find how.
Is there a (relatively) simple way of doing it?
I have tried several approaches:
1) genconf -f dopc128.gro -o dopc_new.gro -nbox 2 2 1
This option can only multiply the by *whole* integer numbers.

2) genconf -f dopc128.gro -o dopc_new.gro -box 1.5X 1.5Y Z # (X and Y
multiplied by 1.5, Z is unchanged).
The dopc_new.gro file will contain X1.5 molecules, but the water
molecules will extend much further than the lipid molecules. So now
there's a small "vacuum" in the gap between upper/lower leaflets of
the membrane in which water can invade.

I would much like to be able to use X1.5 and not X2 since that would
"save" me a whole lot of water/other molecules in the Z-axis, and
therefore simulation time too.

Thanks in advance,
-Shay

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[gmx-users] forcefield for free (neutral) amino acids

[chun feng]

Hi all:

I am not a user of GROMACS, but I hope someone who's working on protein 
dynamics can do me a favor here. I am desperately searching for a forcefield 
for free and neutral amino acids. But it seems that the forcefields such as 
amber and opls only parametrizes amino acids in peptides (without OH and H) and 
terminal amino acids on peptides. I know there has to be some forcefield 
already developed for popular molecules like amino acids, anyone please point 
me the way! Thanks a million!



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[gmx-users] Resizing membrane (dopc, berger)

[shayamra]

Hello dear GROMACS users,

Lately I have been trying to user dopc membrane, using Berger united  
atoms and I am confounded by a problem regarding the size of the  
membrane.
The original membrane from the website is X Y Z (including 128  
lipids). Now I would like to multiply the membrane by 1.5 and I cannot  
find how.

Is there a (relatively) simple way of doing it?
I have tried several approaches:
1) genconf -f dopc128.gro -o dopc_new.gro -nbox 2 2 1
This option can only multiply the by *whole* integer numbers.

2) genconf -f dopc128.gro -o dopc_new.gro -box 1.5X 1.5Y Z # (X and Y  
multiplied by 1.5, Z is unchanged).
The dopc_new.gro file will contain X1.5 molecules, but the water  
molecules will extend much further than the lipid molecules. So now  
there's a small "vacuum" in the gap between upper/lower leaflets of  
the membrane in which water can invade.


I would much like to be able to use X1.5 and not X2 since that would  
"save" me a whole lot of water/other molecules in the Z-axis, and  
therefore simulation time too.


Thanks in advance,
-Shay

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Re: [gmx-users] Identical energies generated in a rerun calculation ... but ...

[David van der Spoel]

Justin A. Lemkul wrote:


Hi Mark,

I tried applying your patch and found some odd installation behavior.  
We have two systems that I am trying to patch.  The first uses gcc-3.3 
and worked fine.  The other uses gcc-4.2.2, and the compilation failed 
with:


"md.c", line 933.18: 1506-046 (S) Syntax error.
"md.c", line 934.11: 1506-277 (S) Syntax error: possible missing ';' or 
','?

make[3]: *** [md.o] Error 1
make[3]: Leaving directory `/home/rdiv1001/gmx/gromacs-4.0.4/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/rdiv1001/gmx/gromacs-4.0.4/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/rdiv1001/gmx/gromacs-4.0.4/src'
make: *** [all-recursive] Error 1

The error seems to point to this line:

 } else { // DDMASTER(cr->dd) == TRUE

Is the statement at the end supposed to be a comment?  I'm only a novice 
at C, so I'm used to seeing something more like:


 } else { /* DDMASTER(cr->dd) == TRUE */

If I make that change, then the system using gcc-4.2.2 doesn't complain 
and the installation finishes successfully.  I don't want to go 
haphazardly commenting out lines of code, so I'd appreciate any feedback 
on what might be going on.


// style comments are C++ only. They are not allowed in GROMACS for this 
reason.




Thanks!

-Justin

Mark Abraham wrote:

Mark Abraham wrote:

Berk Hess wrote:

Hi,

I think you can replace all state-> by state_global-> within { } 
after the if statement

on line 929 of md.c.
Then I think it should work for serial, PD and DD.

Mark, could you test if this works and report back?


Thanks for the prompt response.

I had tried something equivalent to this earlier, and kept getting 
the same segfault. I now see why... state_global is only allocated on 
DDMASTER(cr) (or some such), so we need a slightly more cunning 
solution. I'll figure it out tomorrow.


OK I have a complete fix. Under DD, non-DDMASTER processes should skip 
this step copying data structures from rerun_fr to state_global. The 
sizes of the various loop copies should be state_global->natoms, not 
mdatoms->nr (which is smaller than state_global->natoms under DD, but 
equal under other conditions). So attached is a patchfile to be 
applied from src/kernel with


patch md.c < dd_mdrun.patch

I tested single-processor with and without mpi, four processors with 
DD and no separate PME nodes, four processors with PD, and 16 
processors with DD and 5 PME nodes and got agreement between the 
leading significant figures reported in the .log file for all cases 
compared with single-processor plain 4.0.4.


I had a quick look at CVS releases-4.0-patches and since this bit of 
do_md() looks the same, this patch can probably be applied there 
and/or to the head 4.1 branch painlessly.


I will attach this patchfile to the bugzilla.

Before a release of 4.0.5 or 4.1, normal users should do "mdrun -rerun 
-pd", unless they're confident with applying this patch!


Mark




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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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Re: [gmx-users] Identical energies generated in a rerun calculation ... but ...

[Justin A. Lemkul]

Hi Mark,

I tried applying your patch and found some odd installation behavior.  We have 
two systems that I am trying to patch.  The first uses gcc-3.3 and worked fine. 
 The other uses gcc-4.2.2, and the compilation failed with:


"md.c", line 933.18: 1506-046 (S) Syntax error.
"md.c", line 934.11: 1506-277 (S) Syntax error: possible missing ';' or ','?
make[3]: *** [md.o] Error 1
make[3]: Leaving directory `/home/rdiv1001/gmx/gromacs-4.0.4/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/rdiv1001/gmx/gromacs-4.0.4/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/rdiv1001/gmx/gromacs-4.0.4/src'
make: *** [all-recursive] Error 1

The error seems to point to this line:

 } else { // DDMASTER(cr->dd) == TRUE

Is the statement at the end supposed to be a comment?  I'm only a novice at C, 
so I'm used to seeing something more like:


 } else { /* DDMASTER(cr->dd) == TRUE */

If I make that change, then the system using gcc-4.2.2 doesn't complain and the 
installation finishes successfully.  I don't want to go haphazardly commenting 
out lines of code, so I'd appreciate any feedback on what might be going on.


Thanks!

-Justin

Mark Abraham wrote:

Mark Abraham wrote:

Berk Hess wrote:

Hi,

I think you can replace all state-> by state_global-> within { } 
after the if statement

on line 929 of md.c.
Then I think it should work for serial, PD and DD.

Mark, could you test if this works and report back?


Thanks for the prompt response.

I had tried something equivalent to this earlier, and kept getting the 
same segfault. I now see why... state_global is only allocated on 
DDMASTER(cr) (or some such), so we need a slightly more cunning 
solution. I'll figure it out tomorrow.


OK I have a complete fix. Under DD, non-DDMASTER processes should skip 
this step copying data structures from rerun_fr to state_global. The 
sizes of the various loop copies should be state_global->natoms, not 
mdatoms->nr (which is smaller than state_global->natoms under DD, but 
equal under other conditions). So attached is a patchfile to be applied 
from src/kernel with


patch md.c < dd_mdrun.patch

I tested single-processor with and without mpi, four processors with DD 
and no separate PME nodes, four processors with PD, and 16 processors 
with DD and 5 PME nodes and got agreement between the leading 
significant figures reported in the .log file for all cases compared 
with single-processor plain 4.0.4.


I had a quick look at CVS releases-4.0-patches and since this bit of 
do_md() looks the same, this patch can probably be applied there and/or 
to the head 4.1 branch painlessly.


I will attach this patchfile to the bugzilla.

Before a release of 4.0.5 or 4.1, normal users should do "mdrun -rerun 
-pd", unless they're confident with applying this patch!


Mark




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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] ffgmx:diffusion of oxygen

[David van der Spoel]

Jochen Hub wrote:

Could it be that you have not removed the jumps due to the periodic
boudary conditions before using g_msd?

Try

trjconv -pbc nojump

Jochen


Sunil Thapa wrote:

Respectable Justin/David/Mark
I used ffgmx force field thinking it as suitable for bonds in the oxygen 
molecule. And yes it gives diffusion coefficient of SPC water to be 3.5 which 
matches with that given in the gromacs manual. After equilibrating my system of 
1 oxygen and 255 water molecules in NPT ensemble at 1 bar and 298 K i subjected 
it to the NVT ensemble for about 50 ns. The msd is not a straight line. It 
increases linearly for first 20 ns and after some ns it decreases linearly 
giving negative diffusion coefficient. Could you help me out with it? The model 
contains L-J interaction between oxygen and water molecule. The mdp file used 
for production run is as follows:



This is probably due to poor statistics. g_mds corrects for PBC. 
Simulate a few 100 ns, then you know more.




;RUN CONTROL parameters.
integrator = md
dt = 0.002 ; ps !
nsteps = 5000 ; total 1 ns.
nstcomm = 1
;LANGEVIN DYNAMICS parameters have not been specified as the integrator is 
;md

;OUPUT CONTROL parameters.
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 100
nstenergy = 100
energygrps = OMOL SOL
;NEIGHBOUR SEARCHING parameters.
nstlist = 10
ns_type = grid
rlist = 0.9 ;initially 1 I modified to 0.9
;ELECTROSTATIC and VdW parameters.
rcoulomb = 0.9
rvdw = 0.9
epsilon-r = 1 
;BERENDSEN TEMPERATURE COUPLING is on in two groups

Tcoupl = berendsen
tc-grps = OMOL SOL
tau_t = 0.001 0.01
ref_t = 298 298
;PRESSURE COUPLING is on
Pcoupl = no;berendsen; berendsen exponential relaxation coupling
tau_p = 0.1;modified from 0.5 
compressibility = 4.6e-5

ref_p = 1.0
;SIMULATED ANNEALING parameters are not specified.
;GENERATE VELOCITIES is on at 298 K.
gen_vel = no; ; generate initially
gen_temp = 298
gen_seed = 173529 ;give different values for different trials.
;BONDS parameters
constraints = all-bonds
constraint-algorithm = shake
unconstrained-start = yes
 
and the msd curve is attached in the next mail due to insufficient space

Your help is necessary for me.
Sunil Kumar Thapa
Tribhuvan University, Nepal
 
 



  





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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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Re: [gmx-users] mdrun error

[Justin A. Lemkul]

Pawan Kumar wrote:

probably a bad starting structure...
check this website for  pressure scaling warning : 
http://wiki.gromacs.org/index.php/Errors




Also,

compressibility =  4.575e-4

is of the wrong magnitude for water.  Should be e-5.

-Justin


regards,
pawan

On Mon, Apr 27, 2009 at 5:21 PM, Sheetal Arora 
mailto:sheetal.aror...@gmail.com>> wrote:


I am trying to run the simulation of protein ligand complex.
But after running the mdrun by giving command-"grompp –f md.
mdp –c pr.gro –p trp.top –o md.tpr "
and then "nohup mdrun –deffnm md & "
the md.log file is showing the following message-
Step 11  Warning: pressure scaling more than 1%, mu: 1.01684 1.01684
1.01684

Step 13  Warning: pressure scaling more than 1%, mu: 0.947161
0.947161 0.947161

Step 14  Warning: pressure scaling more than 1%, mu: 1.01207 1.01207
1.01207

Step 15  Warning: pressure scaling more than 1%, mu: 1.18248 1.18248
1.18248

Step 16  Warning: pressure scaling more than 1%, mu: 0.867467
0.867467 0.867467

Step 16, time 0.032 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.099556 (between atoms 1396 and 1398) rms 0.028595
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 21 23   30.80.1740   0.1569  0.1470
 38 40   32.00.1740   0.1583  0.1470
 54 56   33.00.1740   0.1588  0.1470
 56 57   30.60.1810   0.1623  0.1530
 67 69   31.40.1740   0.1568  0.1470
104106   32.60.1740   0.1588  0.1470
106107   31.10.1811   0.1632  0.1530
216218   31.80.1741   0.1584  0.1470
I am attaching my md.mdp file.Please help me in this regard.

-- 
Sheetal Arora

M.Tech(Biotechnology & Medical Engg)

NIT Rourkela

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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] mdrun error

[Pawan Kumar]

probably a bad starting structure...
check this website for  pressure scaling warning :
http://wiki.gromacs.org/index.php/Errors

regards,
pawan

On Mon, Apr 27, 2009 at 5:21 PM, Sheetal Arora wrote:

> I am trying to run the simulation of protein ligand complex.
> But after running the mdrun by giving command-"grompp –f md.
> mdp –c pr.gro –p trp.top –o md.tpr "
> and then "nohup mdrun –deffnm md & "
> the md.log file is showing the following message-
> Step 11  Warning: pressure scaling more than 1%, mu: 1.01684 1.01684
> 1.01684
>
> Step 13  Warning: pressure scaling more than 1%, mu: 0.947161 0.947161
> 0.947161
>
> Step 14  Warning: pressure scaling more than 1%, mu: 1.01207 1.01207
> 1.01207
>
> Step 15  Warning: pressure scaling more than 1%, mu: 1.18248 1.18248
> 1.18248
>
> Step 16  Warning: pressure scaling more than 1%, mu: 0.867467 0.867467
> 0.867467
>
> Step 16, time 0.032 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.099556 (between atoms 1396 and 1398) rms 0.028595
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>  21 23   30.80.1740   0.1569  0.1470
>  38 40   32.00.1740   0.1583  0.1470
>  54 56   33.00.1740   0.1588  0.1470
>  56 57   30.60.1810   0.1623  0.1530
>  67 69   31.40.1740   0.1568  0.1470
> 104106   32.60.1740   0.1588  0.1470
> 106107   31.10.1811   0.1632  0.1530
> 216218   31.80.1741   0.1584  0.1470
> I am attaching my md.mdp file.Please help me in this regard.
>
> --
> Sheetal Arora
> M.Tech(Biotechnology & Medical Engg)
>
> NIT Rourkela
>
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[gmx-users] mdrun error

[Sheetal Arora]

I am trying to run the simulation of protein ligand complex.
But after running the mdrun by giving command-"grompp –f md.
mdp –c pr.gro –p trp.top –o md.tpr "
and then "nohup mdrun –deffnm md & "
the md.log file is showing the following message-
Step 11  Warning: pressure scaling more than 1%, mu: 1.01684 1.01684 1.01684

Step 13  Warning: pressure scaling more than 1%, mu: 0.947161 0.947161
0.947161

Step 14  Warning: pressure scaling more than 1%, mu: 1.01207 1.01207 1.01207

Step 15  Warning: pressure scaling more than 1%, mu: 1.18248 1.18248 1.18248

Step 16  Warning: pressure scaling more than 1%, mu: 0.867467 0.867467
0.867467

Step 16, time 0.032 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.099556 (between atoms 1396 and 1398) rms 0.028595
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 21 23   30.80.1740   0.1569  0.1470
 38 40   32.00.1740   0.1583  0.1470
 54 56   33.00.1740   0.1588  0.1470
 56 57   30.60.1810   0.1623  0.1530
 67 69   31.40.1740   0.1568  0.1470
104106   32.60.1740   0.1588  0.1470
106107   31.10.1811   0.1632  0.1530
216218   31.80.1741   0.1584  0.1470
I am attaching my md.mdp file.Please help me in this regard.

-- 
Sheetal Arora
M.Tech(Biotechnology & Medical Engg)

NIT Rourkela


md.mdp
Description: Binary data
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Re: [gmx-users] ffgmx:diffusion of oxygen

[Jochen Hub]

Could it be that you have not removed the jumps due to the periodic
boudary conditions before using g_msd?

Try

trjconv -pbc nojump

Jochen


Sunil Thapa wrote:
> Respectable Justin/David/Mark
> I used ffgmx force field thinking it as suitable for bonds in the oxygen 
> molecule. And yes it gives diffusion coefficient of SPC water to be 3.5 which 
> matches with that given in the gromacs manual. After equilibrating my system 
> of 1 oxygen and 255 water molecules in NPT ensemble at 1 bar and 298 K i 
> subjected it to the NVT ensemble for about 50 ns. The msd is not a straight 
> line. It increases linearly for first 20 ns and after some ns it decreases 
> linearly giving negative diffusion coefficient. Could you help me out with 
> it? The model contains L-J interaction between oxygen and water molecule. The 
> mdp file used for production run is as follows:
> 
> ;RUN CONTROL parameters.
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 5000 ; total 1 ns.
> nstcomm = 1
> ;LANGEVIN DYNAMICS parameters have not been specified as the integrator is 
> ;md
> ;OUPUT CONTROL parameters.
> nstxout = 250
> nstvout = 1000
> nstfout = 0
> nstlog = 100
> nstenergy = 100
> energygrps = OMOL SOL
> ;NEIGHBOUR SEARCHING parameters.
> nstlist = 10
> ns_type = grid
> rlist = 0.9 ;initially 1 I modified to 0.9
> ;ELECTROSTATIC and VdW parameters.
> rcoulomb = 0.9
> rvdw = 0.9
> epsilon-r = 1 
> ;BERENDSEN TEMPERATURE COUPLING is on in two groups
> Tcoupl = berendsen
> tc-grps = OMOL SOL
> tau_t = 0.001 0.01
> ref_t = 298 298
> ;PRESSURE COUPLING is on
> Pcoupl = no;berendsen; berendsen exponential relaxation coupling
> tau_p = 0.1;modified from 0.5 
> compressibility = 4.6e-5
> ref_p = 1.0
> ;SIMULATED ANNEALING parameters are not specified.
> ;GENERATE VELOCITIES is on at 298 K.
> gen_vel = no; ; generate initially
> gen_temp = 298
> gen_seed = 173529 ;give different values for different trials.
> ;BONDS parameters
> constraints = all-bonds
> constraint-algorithm = shake
> unconstrained-start = yes
>  
> and the msd curve is attached in the next mail due to insufficient space
> Your help is necessary for me.
> Sunil Kumar Thapa
> Tribhuvan University, Nepal
>  
>  
> 
> 
>   
> 
> 
> 
> 
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-- 

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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Re: [gmx-users] Steepest Descents converged to machine precision

[Mark Abraham]

nitu sharma wrote:

Dear mark


But how can it possible that starting structure is grossly broken , up 
to infltegro first step I enquired my structure It looks fine but after 
doing enegy minimisation step i saw that structure is disturbed


OK so what can you deduce from that? It was fine, and then some forces 
acted on it...


May be its due to restrain not working on protein . To apply position 


So simplify your problem - don't use the restraints, and see what happens.

restrain on protein I have edited posre.itp file with force constant 
10 and included it in topology file-

 Include forcefield parameters
#include "ffG53a6_lipid.itp"

#include "topol_A.itp"
#ifdef POSRES
#include "posre_A.itp

#include "topol_B.itp
#ifdef POSRES
#include "posre_B.itp
#endif

But its not working .
I am unable to understand why?


The above is nonsense. You haven't matched #ifdef with #endif, or 
opening with closing quotation marks.


Mark
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[gmx-users] Steepest Descents converged to machine precision

[nitu sharma]

Dear mark


But how can it possible that starting structure is grossly broken , up to
infltegro first step I enquired my structure It looks fine but after doing
enegy minimisation step i saw that structure is disturbed
May be its due to restrain not working on protein . To apply position
restrain on protein I have edited posre.itp file with force constant 10
and included it in topology file-
 Include forcefield parameters
#include "ffG53a6_lipid.itp"

#include "topol_A.itp"
#ifdef POSRES
#include "posre_A.itp

#include "topol_B.itp
#ifdef POSRES
#include "posre_B.itp
#endif

But its not working .
I am unable to understand why?

can u give me some idea about that?

NITU sharma
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Re: [gmx-users] ffgmx:diffusion of oxygen

[Mark Abraham]

Sunil Thapa wrote:

Respectable Justin/David/Mark
I used ffgmx force field thinking it as suitable for bonds in the oxygen 
molecule. And yes it gives diffusion coefficient of SPC water to be 3.5 
which matches with that given in the gromacs manual. After equilibrating 
my system of 1 oxygen and 255 water molecules in NPT ensemble at 1 bar 
and 298 K i subjected it to the NVT ensemble for about 50 ns. The msd is 
not a straight line. It increases linearly for first 20 ns and after 
some ns it decreases linearly giving negative diffusion coefficient. 
Could you help me out with it? The model contains L-J interaction 
between oxygen and water molecule. The mdp file used for production run 
is as follows:

;RUN CONTROL parameters.
integrator = md
dt = 0.002 ; ps !
nsteps = 5000 ; total 1 ns.
nstcomm = 1
;LANGEVIN DYNAMICS parameters have not been specified as the integrator is
;md
;OUPUT CONTROL parameters.
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 100
nstenergy = 100
energygrps = OMOL SOL
;NEIGHBOUR SEARCHING parameters.
nstlist = 10
ns_type = grid
rlist = 0.9 ;initially 1 I modified to 0.9
;ELECTROSTATIC and VdW parameters.
rcoulomb = 0.9
rvdw = 0.9
epsilon-r = 1
;BERENDSEN TEMPERATURE COUPLING is on in two groups
Tcoupl = berendsen
tc-grps = OMOL SOL


http://wiki.gromacs.org/index.php/Thermostats


tau_t = 0.001 0.01
ref_t = 298 298
;PRESSURE COUPLING is on
Pcoupl = no;berendsen; berendsen exponential relaxation coupling
tau_p = 0.1;modified from 0.5
compressibility = 4.6e-5
ref_p = 1.0
;SIMULATED ANNEALING parameters are not specified.
;GENERATE VELOCITIES is on at 298 K.
gen_vel = no; ; generate initially
gen_temp = 298
gen_seed = 173529 ;give different values for different trials.
;BONDS parameters
constraints = all-bonds
constraint-algorithm = shake
unconstrained-start = yes
 
and the msd curve is attached in the next mail due to insufficient space

Your help is necessary for me.
Sunil Kumar Thapa
Tribhuvan University, Nepal
 
 






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[gmx-users] validating gromacs installation 4.0.4

[Rafael R. Pappalardo]

Dear Sasidhar,
I am getting the same errors from the gmxtest.pl command.
./gmxtest.pl all
All 16 simple tests PASSED
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in tip4pflex
FAILED. Check files in water
4 out of 14 complex tests FAILED
FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED

 I have tried yours patches but, in my system (Gromacs-4.0.4 compiled with 
Intel compilers IA-64 11.0.081 single precision), I only need to change 
rlist=rcoulomb in the kernel's grompp.mpd files to make them not to fail.

Thanks a lot for your analysis.

Sincerely,

Rafael
-- 
Dr. Rafael R. Pappalardo
Physical Chemistry Dept., Univ. de Sevilla (Spain)
e-mail: raf...@us.es
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[gmx-users] ffgmx:diffusion of oxygen

[Sunil Thapa]

Respectable Justin/David/Mark
I used ffgmx force field thinking it as suitable for bonds in the oxygen 
molecule. And yes it gives diffusion coefficient of SPC water to be 3.5 which 
matches with that given in the gromacs manual. After equilibrating my system of 
1 oxygen and 255 water molecules in NPT ensemble at 1 bar and 298 K i subjected 
it to the NVT ensemble for about 50 ns. The msd is not a straight line. It 
increases linearly for first 20 ns and after some ns it decreases linearly 
giving negative diffusion coefficient. Could you help me out with it? The model 
contains L-J interaction between oxygen and water molecule. The mdp file used 
for production run is as follows:

;RUN CONTROL parameters.
integrator = md
dt = 0.002 ; ps !
nsteps = 5000 ; total 1 ns.
nstcomm = 1
;LANGEVIN DYNAMICS parameters have not been specified as the integrator is 
;md
;OUPUT CONTROL parameters.
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 100
nstenergy = 100
energygrps = OMOL SOL
;NEIGHBOUR SEARCHING parameters.
nstlist = 10
ns_type = grid
rlist = 0.9 ;initially 1 I modified to 0.9
;ELECTROSTATIC and VdW parameters.
rcoulomb = 0.9
rvdw = 0.9
epsilon-r = 1 
;BERENDSEN TEMPERATURE COUPLING is on in two groups
Tcoupl = berendsen
tc-grps = OMOL SOL
tau_t = 0.001 0.01
ref_t = 298 298
;PRESSURE COUPLING is on
Pcoupl = no;berendsen; berendsen exponential relaxation coupling
tau_p = 0.1;modified from 0.5 
compressibility = 4.6e-5
ref_p = 1.0
;SIMULATED ANNEALING parameters are not specified.
;GENERATE VELOCITIES is on at 298 K.
gen_vel = no; ; generate initially
gen_temp = 298
gen_seed = 173529 ;give different values for different trials.
;BONDS parameters
constraints = all-bonds
constraint-algorithm = shake
unconstrained-start = yes
 
and the msd curve is attached in the next mail due to insufficient space
Your help is necessary for me.
Sunil Kumar Thapa
Tribhuvan University, Nepal
 
 


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Re: [gmx-users] which structure in NPT MD trjectory should be chosen to start another NVT MD?

[Mark Abraham]

wuxiao wrote:
> Dear gmx users,
>   Usually, we perform NPT MD to achieve optimized density of system and 
> start another NVT MD to calculate other properties of interest.  I think 
> there are three possible ways to choose the structure to start another 
> NVT MD:(1) the structure of last step in NPT MD trjectory;(2)the 
> structure in NPT MD trjectory with the density closest to the averaging 
> density;(3)the structure of last step in NPT MD trjectory but the box 
> size needs to be rescaled so that it is the averaging size. My question 
> is: which way should be chosen to start another NVT MD? I do not know 
> whether this question is suitable here. Any hints would be thanked very 
> much.

Bear in mind in your averaging that you're actually interested in the
average *after* equilibration, which often does not include the start of
a trajectory.

Otherwise, I think it's largely irrelevant except that you don't want a
density that's noticeably different from the one used in
parameterization of the forcefield. You'll still need a period of
further equilibration after any of the above choices.

Mark
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Re: [gmx-users] Steepest Descents converged to machine precision

[Mark Abraham]

nitu sharma wrote:

Dear Mark

I explain you what I  want to ask . I give you a detail of my processing -
* step for packing lipid around protein-
1. concatanation of protein and lipid bilayer in proper orientation- I did.
2.Inflate the bilayer by using inflategro script with scaling factor 4 
and cutoff 14- I did .
 there is 8 lipid removed in this process and a/c to that   I have 
update my topology file .
3. Energy minimisation by applying strong position restrain on protein 
the force constant=10


problem occur here is-

Step=  344, Dmax= 1.8e-05 nm, Epot=  4.29315e+06 Fmax= 1.02525e+05, 
atom= 4615
Step=  349, Dmax= 1.4e-06 nm, Epot=  4.29315e+06 Fmax= 9.86524e+04, 
atom= 4615

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 350 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  4.2931510e+06
Maximum force =  1.0252509e+05 on atom 4615
Norm of force =  1.3668822e+03


These are so large or positive that your starting structure is grossly 
broken. You need to find out why. Look at the structures at each point 
of your procedure.


Mark
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[gmx-users] which structure in NPT MD trjectory should be chosen to start another NVT MD?

[wuxiao]

Dear gmx users,

  Usually, we perform NPT MD to achieve optimized density of system and start 
another NVT MD to calculate other properties of interest.  I think there are 
three possible ways to choose the structure to start another NVT MD:(1) the 
structure of last step in NPT MD trjectory;(2)the structure in NPT MD trjectory 
with the density closest to the averaging density;(3)the structure of last step 
in NPT MD trjectory but the box size needs to be rescaled so that it is the 
averaging size. My question is: which way should be chosen to start another NVT 
MD? I do not know whether this question is suitable here. Any hints would be 
thanked very much.

Best wishes,

xiaowu

 

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[gmx-users] Steepest Descents converged to machine precision

[nitu sharma]

Dear Mark

I explain you what I  want to ask . I give you a detail of my processing -
* step for packing lipid around protein-
1. concatanation of protein and lipid bilayer in proper orientation- I did.
2.Inflate the bilayer by using inflategro script with scaling factor 4 and
cutoff 14- I did .
 there is 8 lipid removed in this process and a/c to that   I have update my
topology file .
3. Energy minimisation by applying strong position restrain on protein the
force constant=10

problem occur here is-

Step=  344, Dmax= 1.8e-05 nm, Epot=  4.29315e+06 Fmax= 1.02525e+05, atom=
4615
Step=  349, Dmax= 1.4e-06 nm, Epot=  4.29315e+06 Fmax= 9.86524e+04, atom=
4615
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 350 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  4.2931510e+06
Maximum force =  1.0252509e+05 on atom 4615
Norm of force =  1.3668822e+03

my em.mdp file-
cpp =  /usr/bin/cpp
define  =  -DPOSRES
constraints =  none
integrator  =  steep
nsteps  =  1
;
;   Energy minimizing stuff
;
emtol   =  1000
emstep  =  0.001

nstcomm =  1
ns_type =  grid
rlist   =  1
rcoulomb=  1.0
rvdw=  1.0
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no
comm-mode   = Linear
pbc = XYZ

my topology file is like this-
; Include forcefield parameters
#include "ffG53a6_lipid.itp"

#include "topol_A.itp"
#ifdef POSRES
#include "posre_A.itp

#include "topol_B.itp
#ifdef POSRES
#include "posre_B.itp
#endif

; Include DMPC chain topology
#include "dmpc.itp"

[ system ]
; Name
Protein in DMPC bilayer

[ molecules ]
; Compound#mols
Protein_A   1
Protein_B   1
DMPC   120

my question-
1. probable reason of steepest descent converged to macine precision  but
did not reach the requested Fmax < 1000.
2.The even after applying strong position restrain on protein the protein
structure being disturbed.

If u can make help for me . I will appreciate you.

Thanks
Nitu sharma
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[gmx-users] Re:(Mark) The X-size of the box times triclinic skew factor is smaller than ...

[wuxiao]

Dear Mark,
  Thank you very much for the quick reply. According to your suggesstion, I had 
a look at the structure or trajectory using ngmx. Only to find that there are 
some big hole in the center, which seems to indicate the system is very 
inhomogeneous. And the system volume  decreased slowly.  when I using cutoff 
instead of PME for columbic force, and change the cutoff from 1.4 to 1.0, the 
mdrun finished 300 ps successfully. Another 3ns is started to try whether it 
can succeed too. more help from these descriptions?
Best regards,
xiaowu
 

wuxiao wrote:
> Dear Mark,
> Thank you for your reply. The system I simulated was one Polymer 
> chain solvated by 200 water that had totally about 3000 atoms. I had 
> defined the system density as 1000 using editconf.

That just does a scaling. It might not fix a gross problem, so do look
at the box dimensions before and after.

> This density was very 
> the experimental one. After enough minimization (convergent to 0.1 
> kj/mol) and 3 ns of NVT MD, the NPT MD was performed as describe in the 
> original question. It happened to terminate with the fatal error after 
> about 300 ps. It should be noted that I ran the mpimdrun using the 
> following command:
> mpirun -np 4 mpimdrun -s 03md.tpr -c poly_md.gro -v
> I have a four-core CPU. Can you give more help according to these 
> descriptions?

Your preparation seems good enough not to be the source of the problem.

Have a look at the trajectory. What does the structure look like? What
is happening to the box dimensions and/or density (look in the .log file
and/or use g_energy)?.

I believe that the error message you're getting is consistent with a
drastic decrease in the box size. Since EM and NVT don't break and NPT
does, the most likely hypothesis is that it started far too large.

Mark

> Best regards,
> xiaowu
> 
> wuxiao wrote:
> > >Dear gmx users,
> > >While doing a NPT molecular dynamics(MD), A fatal error was given:
> > >The X-size of the box times triclinic skew factor is smaller than the
> > >number of DD cells times the smallest allowed cell size.
> > >However, either NVT or NVE MD can work well. Can you give any help to
> > >deal with this problem?
> 
> >It sounds like you might have started with a density that is too low for
> >your box size.
> 
> >A more complete description of your system and what you've done with it
> >might help you get useful advice.
> 
> Mark
> 
> 
> 



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Re: [gmx-users] steepest descents converged to machine precision in several steps.

[Mark Abraham]

nitu sharma wrote:

Dear Mark

 Thanks for replying. one thing I want to ask i.e can u explain 
me in brief way why steepest descent converted into machine precision 
and E.M can't completed total step given in parameter file .
One thing happen during this i.e even after applying position restrain 
force constant-10 ,the protein structure being disturbed .


Please help me in solving these two problem.


I can't understand what you're asking.

EM is like playing blindfold golf. Even if you know you're in a bunker 
and you know how big the bunker is, you still don't know the direction 
of the green or how hard to swing the club to get the ball onto it.


In some ways EM is harder than golf... if you aren't swinging the club 
hard enough, you won't always know you're still in the same bunker.


Mark
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[gmx-users] steepest descents converged to machine precision in several steps.

[nitu sharma]

Dear Mark

 Thanks for replying. one thing I want to ask i.e can u explain me
in brief way why steepest descent converted into machine precision and E.M
can't completed total step given in parameter file .
One thing happen during this i.e even after applying position restrain force
constant-10 ,the protein structure being disturbed .

Please help me in solving these two problem.

THANKS
NITU SHARMA
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