[gmx-users] Fw: Re: Re: ionic liquids

[Prema Awati]

 








-- Original Message --

From: prem...@iiserpune.ac.in

To: vvcha...@gmail.com

Date: Tue, 3 May 2011 11:30:00 +0530 (GMT+05:30)

Subject: Re: Re: ionic liquids



Sir,



Thanks for your response !!



The LJ parameters are defined in forcefield 
database so it need not require to be mentioned in topology,I followed gromacs 
manual.But If its working by adding in the topology,then please guide me 
regarding LJ parameters. I used OPLS forcefield to create raw topology and then 
edited referring Tsuzuki"s.



Tsuzuki et.al used basically Lopes et.al 
forcefield which was refined(partial charges,nonbonding parameters ) to 
reproduce experimental density.



I obtained 1.0045 g/cm3 density which is poor 
to do final production run in order to study diffusive dynamics of ionic 
liquids, so I am looking to get exact density that of Tsuzuki.



Thanks.











-- Original 
Message --

From: Vitaly 
Chaban 

To: Prema Awati 


Cc: 
gmx-users@gromacs.org

Date: Mon, 2 
May 2011 15:00:19 -0400

Subject: Re: 
ionic liquids



Where are your 
LJ parameters? 







Are you 
sure that Tsuzuki uses all standard OPLS parameters?







What 
density do you get in your simulation?












--


Dr. Vitaly V. Chaban, Department of Chemistry


University of Rochester, Rochester, New York 14627-0216



















On Mon, May 2,

[gmx-users] g_select is pretty fantastic

[chris . neale]

Dear g_select developers:

This is a shout out of thanks for this new tool, which I find very useful.

For users who have not played around with this, I'd suggest trying it  
(especially if you are already familiar with VMD-style selection  
syntax).


I want to make special thanks for the VMD-style selection language,  
which avoids us all having to learn yet another protocol. I would  
suggest direct interaction between the g_select developers and the VMD  
developers to bring this into lock-step over the coming years (perhaps  
a universal selection syntax?). Another suggestion is that I only  
realized that the syntax is essentially a VMD-syntax by trying it out  
(there is no documentation that mentions this). I'm thus not sure how  
overlapping the syntaxes really are, but would request that they  
become fully-overlapping over time and that the current possibilities  
are mentioned in the help information.


Another important note is that you need to supply a .ndx file from a  
simple run through make_ndx to get things to work like "group  
Protein". I think it was a good decision to wall-off the creation of  
standard selection groups (make_ndx) from the g_select program, but I  
think that this fact would be useful in the documentation.


To be more explicit about the possibilities, one can do things like:

GRO=indo.1.2.6.5us.gro;
echo -e "aP8\nq\n" | make_ndx -f ${GRO} -o initial.ndx;
g_select -f ${GRO} -n initial.ndx -on select.ndx -select "same residue  
as group P8 and within 1 of group Protein" -s full.tpr;


Pretty cool.

Thanks again,
Chris.

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[gmx-users] tabulated potentials for non-bonded interactions

[Sikandar Mashayak]

Hi

Is it possible to use use specified potentials only for vdw type non-bonded
interactions while keeping usual PME,bonded, pairs interactions?

When I specifiy "User" for vdwtype force in .mdp file, I am observing that
mdrun expects table for bonded interactions also through -tableb option and
by default uses table.xvg. Is there any way to avoid this?

thanks
sikandar
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Re: [gmx-users] Re: Unsteady Density

[Justin A. Lemkul]

Fabian Casteblanco wrote:

Thanks Justin.

I'm currently running the MD run separately so that the average value
won't be affected by the unequilibrated values at the beginning of the
NPT run where the density started in the 400s and ran up to the ~high
700s.  I had done this before when I had nstlist at 5 but I did run
NPT for a lot shorter time last time so Im hoping this time it will be
better since last time it was still off (0.781 g/cm3 to 0.791 g.cm3).
I will also change the compressibility.  Do you think increasing the
rlist, rcoulomb, rvdw value to about 1.6, 1.8 nm might also work a bit
better?



No, in fact it will probably make it worse.  Use the values prescribed by the 
force field.


-Justin


Thanks again.

On Mon, May 2, 2011 at 2:16 PM, Fabian Casteblanco
 wrote:

Hello,

I have been trying to use CHARMM forcefield to simulate 1000 molecules
of Methanol in a box but I seem to fall short on the density every
time I run.  At first, I had my rlist at 1 but CHARMM recommends
greater than 1.2-1.4 nm so I changed accordingly, then I changed it so
that the short neighbor list would update more freqently and finally I
even added a greater amount of steps, hoping that the pressure and
density would settle down at some value.

Below, I had taken and modified from the Lysozyme tutorial.  One thing
I noticed is the contraint -algorithm and how the constraints are set
to 'all-bonds'.  Is this necessary?  After running NVT (leveled off
near 298K, seemed ok), then NPT, for 300,000 steps, the pressure is
close to the reference 1 bar, ~1.1,1.2 bar, but I noticed the density
is still oscillating, not by much, but it still leaves me questioning
why its not settling around to the literature value of 0.791 g/cm3.  I
posted the last several lines from the analysis *.xvg file.  NPT
script is also below.

Is there still more steps that I have to run for?  The density just
seems to be oscillating too much and although a literature value of
0.791 g/cm3 is within the data, it doesnt seem to be settling around
that value.  I have similar problems for 1-propanol to where my
simulated density is under that of the literature value.  Could it be
possible that maybe I should use different NVT, NPT algorithms
(tcoupl, pcoupl)?

I would really appreciate anyones help. I'm still in my first few
months of learning the program.  Thanks!

 591.80  38039.125000  297.409546  -206.071747  779.428894
 592.00  38035.421875  294.95  -20.557419  777.816956
 592.20  37982.812500  298.063324  -463.192047  776.430542
 592.40  37681.421875  295.430878   36.529854  776.460876
 592.60  37476.148438  297.193787  -28.961288  775.634644
 592.80  37611.574219  297.059875  -553.369263  774.096924
 593.00  37682.277344  288.297974  -293.567963  776.055237
 593.20  37147.824219  295.985901  -221.989441  781.570679
 593.40  37404.906250  293.938721  399.093018  788.921570
 593.60  37339.914062  297.464783  415.891235  793.838440
 593.80  37909.019531  292.707184  574.818726  796.730286
 594.00  37369.820312  304.095703  -119.569496  796.235962
 594.20  37293.445312  294.449005  -63.335049  794.578552
 594.40  37196.917969  295.323761  104.148239  791.275085
 594.60  37776.199219  298.004333   28.989655  785.244629
 594.80  37893.097656  302.397308  -268.065765  779.457886
 595.00  38123.460938  295.343109  -140.914047  775.682678
 595.20  38002.054688  302.233124  -91.893478  774.813660
 595.40  37835.652344  297.808319  441.931885  776.142090
 595.60  38103.964844  296.369019  490.766754  778.422302
 595.80  37686.902344  303.358093  -19.726471  781.057922
 596.00  37586.890625  293.751648  -92.387199  783.724854
 596.20  37408.414062  300.007385  -288.156036  785.990417
 596.40  37894.898438  295.720520  346.861206  788.753174
 596.60  37673.378906  288.311432   89.059952  789.179993
 596.80  36881.062500  295.265564   70.789131  791.552673
 597.00  37077.789062  296.261444   72.207787  793.970398
 597.20  37123.230469  296.511475  -232.434616  793.653564
 597.40  37426.152344  304.281891  -133.300797  791.791077
 597.60  37514.332031  305.183197  -259.364136  787.592712
 597.80  37393.667969  301.326111  -150.162338  785.053711
 598.00  37263.054688  299.811554  326.851837  785.553894
 598.20  37203.261719  300.688904  225.526001  788.008667
 598.40  37511.636719  302.506714   66.299194  790.725281
 598.60  37460.843750  299.512909  198.943665  793.35
 598.80  37248.921875  291.575134  -93.283127  793.582703
 599.00  36870.480469  293.515381  211.069107  792.929443
 599.20  37398.097656  293.184448  -163.371140  789.150513
 599.40  37402.238281  297.402008   45.650658  786.303711
 599.60  37419.816406  298.520508  -147.688004  783.492371
 599.80  37497.332031  296.529877  -15.991615  782.294250
 600.00  37691.468750  298.839844  -68.580627  781.974182



title 

[gmx-users] Re: Unsteady Density

[Fabian Casteblanco]

Thanks Justin.

I'm currently running the MD run separately so that the average value
won't be affected by the unequilibrated values at the beginning of the
NPT run where the density started in the 400s and ran up to the ~high
700s.  I had done this before when I had nstlist at 5 but I did run
NPT for a lot shorter time last time so Im hoping this time it will be
better since last time it was still off (0.781 g/cm3 to 0.791 g.cm3).
I will also change the compressibility.  Do you think increasing the
rlist, rcoulomb, rvdw value to about 1.6, 1.8 nm might also work a bit
better?

Thanks again.

On Mon, May 2, 2011 at 2:16 PM, Fabian Casteblanco
 wrote:
> Hello,
>
> I have been trying to use CHARMM forcefield to simulate 1000 molecules
> of Methanol in a box but I seem to fall short on the density every
> time I run.  At first, I had my rlist at 1 but CHARMM recommends
> greater than 1.2-1.4 nm so I changed accordingly, then I changed it so
> that the short neighbor list would update more freqently and finally I
> even added a greater amount of steps, hoping that the pressure and
> density would settle down at some value.
>
> Below, I had taken and modified from the Lysozyme tutorial.  One thing
> I noticed is the contraint -algorithm and how the constraints are set
> to 'all-bonds'.  Is this necessary?  After running NVT (leveled off
> near 298K, seemed ok), then NPT, for 300,000 steps, the pressure is
> close to the reference 1 bar, ~1.1,1.2 bar, but I noticed the density
> is still oscillating, not by much, but it still leaves me questioning
> why its not settling around to the literature value of 0.791 g/cm3.  I
> posted the last several lines from the analysis *.xvg file.  NPT
> script is also below.
>
> Is there still more steps that I have to run for?  The density just
> seems to be oscillating too much and although a literature value of
> 0.791 g/cm3 is within the data, it doesnt seem to be settling around
> that value.  I have similar problems for 1-propanol to where my
> simulated density is under that of the literature value.  Could it be
> possible that maybe I should use different NVT, NPT algorithms
> (tcoupl, pcoupl)?
>
> I would really appreciate anyones help. I'm still in my first few
> months of learning the program.  Thanks!
>
>  591.80  38039.125000  297.409546  -206.071747  779.428894
>  592.00  38035.421875  294.95  -20.557419  777.816956
>  592.20  37982.812500  298.063324  -463.192047  776.430542
>  592.40  37681.421875  295.430878   36.529854  776.460876
>  592.60  37476.148438  297.193787  -28.961288  775.634644
>  592.80  37611.574219  297.059875  -553.369263  774.096924
>  593.00  37682.277344  288.297974  -293.567963  776.055237
>  593.20  37147.824219  295.985901  -221.989441  781.570679
>  593.40  37404.906250  293.938721  399.093018  788.921570
>  593.60  37339.914062  297.464783  415.891235  793.838440
>  593.80  37909.019531  292.707184  574.818726  796.730286
>  594.00  37369.820312  304.095703  -119.569496  796.235962
>  594.20  37293.445312  294.449005  -63.335049  794.578552
>  594.40  37196.917969  295.323761  104.148239  791.275085
>  594.60  37776.199219  298.004333   28.989655  785.244629
>  594.80  37893.097656  302.397308  -268.065765  779.457886
>  595.00  38123.460938  295.343109  -140.914047  775.682678
>  595.20  38002.054688  302.233124  -91.893478  774.813660
>  595.40  37835.652344  297.808319  441.931885  776.142090
>  595.60  38103.964844  296.369019  490.766754  778.422302
>  595.80  37686.902344  303.358093  -19.726471  781.057922
>  596.00  37586.890625  293.751648  -92.387199  783.724854
>  596.20  37408.414062  300.007385  -288.156036  785.990417
>  596.40  37894.898438  295.720520  346.861206  788.753174
>  596.60  37673.378906  288.311432   89.059952  789.179993
>  596.80  36881.062500  295.265564   70.789131  791.552673
>  597.00  37077.789062  296.261444   72.207787  793.970398
>  597.20  37123.230469  296.511475  -232.434616  793.653564
>  597.40  37426.152344  304.281891  -133.300797  791.791077
>  597.60  37514.332031  305.183197  -259.364136  787.592712
>  597.80  37393.667969  301.326111  -150.162338  785.053711
>  598.00  37263.054688  299.811554  326.851837  785.553894
>  598.20  37203.261719  300.688904  225.526001  788.008667
>  598.40  37511.636719  302.506714   66.299194  790.725281
>  598.60  37460.843750  299.512909  198.943665  793.35
>  598.80  37248.921875  291.575134  -93.283127  793.582703
>  599.00  36870.480469  293.515381  211.069107  792.929443
>  599.20  37398.097656  293.184448  -163.371140  789.150513
>  599.40  37402.238281  297.402008   45.650658  786.303711
>  599.60  37419.816406  298.520508  -147.688004  783.492371
>  599.80  37497.332031  296.529877  -15.991615  782.294250
>  600.00  37691.468750  298.839844  -68.580627  781.974182
>
>
>
> title

[gmx-users] Re: Unsteady Density

[Vitaly Chaban]

> The last time I had performed this with nstlist=5 and for the
> actual MD run, I had a density of approximately 0.781 g/cm3 compared
> to literature value of 0.791 g/cm3 at 298K.

So, what is the problem? It is satisfactory coincidence.



-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
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Re: [gmx-users] RE: How to use Inflategro with different lipid types

[Oliver Stueker]

Hi,

I recently came across the CELLmicrocosmos 2.2 MembraneEditor, in
which one can easily generate coordinates for mixed membranes and
AFAIK also insert a protein.

http://cm2.cellmicrocosmos.org/
http://pubs.acs.org/doi/abs/10.1021/ci1003619

I haven't had the chance/need to actually try it, though.

Cheers,
Oliver

2011/5/2 Ioannis Beis :
> Hello,
>
> I would like to thank Justin and Tom for their kind replies to my question!
> I believe that by having the gromacs manual as a guide I would manage to
> bring the bilayer into physiological size by using Justin's advice. However,
> Tom's advice sounds simpler to implement. Unfortunately the size of the
> pre-equilibrated POPC is too small for what I want to do afterwards, but I
> can make my own POPC using editconf, genconf and Inflategro to shrink and
> equilibrate it first and then use the renaming trick.
>
> For beginner users that will consult this thread in the future, I had
> overestimated the value of the coordinate files as starting structures...
> Deleting the last two united atoms from oleoyl will fix the hydrocarbon
> chain length and using a palmitoyl force field will take care of turning the
> double bond into a single one. Renaming the three different united atoms'
> names in the polar heads and eventually the names of the whole lipids is
> like turning ethanolamine into choline and vice versa. The initial positions
> at the crucial points will be very improper, but this isn't important since
> hopefully the energy minimization will fix them. This strategy -with a
> little more work- could even be applied for more diverse polar heads as soon
> as one has a force field, just by placing his atoms at very reasonable
> initial positions! Proper topology file is all that matters :).
>
> Thanks again for your ideas!
>
> Yiannis
>
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Re: [gmx-users] Re: Unsteady Density

[Justin A. Lemkul]

Fabian Casteblanco wrote:

Hello,

Thanks for your response.  Here are my responses to your points:

nstlist=1 is overkill.  I will change this back to 5 except for EM
like you said. I originially thought that maybe the density not
settling was because the neighbor searching frequency had not been
updated frequently enough causing molecule density to change.



Not likely.


When I performed this specific NPT run, the average was off due to the
fact that the density started off in the 400s and rised up to ~high
700s.  The last time I had performed this with nstlist=5 and for the
actual MD run, I had a density of approximately 0.781 g/cm3 compared
to literature value of 0.791 g/cm3 at 298K.  I was getting similar
results for 1-propanol with the difference much greater. I was hoping
that if I could somehow fix the methanol system, I would be able to
fix the 1-propanol system.



If you're taking averages over the whole time, that probably accounts for the 
discrepancy.  The initial values are clearly not correct, and thus those frames 
should be discarded as equilibration.  Block averaging will show you if there 
are any systematic trends in the data (i.e. drifts that indicate you're not yet 
converged).



I created the topologies using the OPLSAA *.itp file (to keep the
structure correctly, bonds, angles, etc) and I reassigned the values
corresponding to CHARMM (attached).  At first, I had placed the values
straight from the literature found on the CHARMM website,
http://mackerell.umaryland.edu/CHARMM_ff_params.html, but I realized
they were nearly identical and were infact the same values in the
CHARMM.ff files in GROMACS (i.e. ffbonded.itp, ffnonbonded.itp)  All I
did was reassign the functions to the functions used in the
ffbonded.itp and ffnonbonded.itp found in CHARMM files on GROMACS.
The charges were all from the CHARMM parameter website that had this
molecule already documented (a copy of the lines is placed at the top
of the *.itp file attached).



Based on the fact that you're taking the parameters straight from CHARMM, I 
don't suspect anything wrong here.



I guess the compressibility factor might make a difference.  The
manual said that the value is fairly close to most liquids so I had
simply ignored the difference but I will look into it.



You're looking at a difference of 1.3% (or less, depending on whether or not you 
include unequilibrated frames in your analysis), so even something that may seem 
trivial could cause this difference.



After reading more up on it, I was thinking maybe accounting for
gradual cutoffs near the ends using rcoulomb_switch and similarly for
rvdw.



Switching functions have their own issues associated with them (discontinuities 
at the longest cutoff), so for now, stick with PME unless you have specific 
reason to use a switching function (i.e., that's how the parameters were 
designed to be used).


Otherwise, this might all be a matter of incorrect analysis, using frames that 
are not supposed to be included.


-Justin


Anything wrong with the way I created the topology?  Dr. Vitaly, I
also attached the *.itp files like you mentioned.

Thanks again for all your help.



On Mon, May 2, 2011 at 2:16 PM, Fabian Casteblanco
 wrote:

Hello,

I have been trying to use CHARMM forcefield to simulate 1000 molecules
of Methanol in a box but I seem to fall short on the density every
time I run.  At first, I had my rlist at 1 but CHARMM recommends
greater than 1.2-1.4 nm so I changed accordingly, then I changed it so
that the short neighbor list would update more freqently and finally I
even added a greater amount of steps, hoping that the pressure and
density would settle down at some value.

Below, I had taken and modified from the Lysozyme tutorial.  One thing
I noticed is the contraint -algorithm and how the constraints are set
to 'all-bonds'.  Is this necessary?  After running NVT (leveled off
near 298K, seemed ok), then NPT, for 300,000 steps, the pressure is
close to the reference 1 bar, ~1.1,1.2 bar, but I noticed the density
is still oscillating, not by much, but it still leaves me questioning
why its not settling around to the literature value of 0.791 g/cm3.  I
posted the last several lines from the analysis *.xvg file.  NPT
script is also below.

Is there still more steps that I have to run for?  The density just
seems to be oscillating too much and although a literature value of
0.791 g/cm3 is within the data, it doesnt seem to be settling around
that value.  I have similar problems for 1-propanol to where my
simulated density is under that of the literature value.  Could it be
possible that maybe I should use different NVT, NPT algorithms
(tcoupl, pcoupl)?

I would really appreciate anyones help. I'm still in my first few
months of learning the program.  Thanks!

 591.80  38039.125000  297.409546  -206.071747  779.428894
 592.00  38035.421875  294.95  -20.557419  777.816956
 592.20  37982.812500  298.063324  -463.192047  776.430542

[gmx-users] Re: Unsteady Density

[Fabian Casteblanco]

Hello,

Thanks for your response.  Here are my responses to your points:

nstlist=1 is overkill.  I will change this back to 5 except for EM
like you said. I originially thought that maybe the density not
settling was because the neighbor searching frequency had not been
updated frequently enough causing molecule density to change.

When I performed this specific NPT run, the average was off due to the
fact that the density started off in the 400s and rised up to ~high
700s.  The last time I had performed this with nstlist=5 and for the
actual MD run, I had a density of approximately 0.781 g/cm3 compared
to literature value of 0.791 g/cm3 at 298K.  I was getting similar
results for 1-propanol with the difference much greater. I was hoping
that if I could somehow fix the methanol system, I would be able to
fix the 1-propanol system.

I created the topologies using the OPLSAA *.itp file (to keep the
structure correctly, bonds, angles, etc) and I reassigned the values
corresponding to CHARMM (attached).  At first, I had placed the values
straight from the literature found on the CHARMM website,
http://mackerell.umaryland.edu/CHARMM_ff_params.html, but I realized
they were nearly identical and were infact the same values in the
CHARMM.ff files in GROMACS (i.e. ffbonded.itp, ffnonbonded.itp)  All I
did was reassign the functions to the functions used in the
ffbonded.itp and ffnonbonded.itp found in CHARMM files on GROMACS.
The charges were all from the CHARMM parameter website that had this
molecule already documented (a copy of the lines is placed at the top
of the *.itp file attached).

I guess the compressibility factor might make a difference.  The
manual said that the value is fairly close to most liquids so I had
simply ignored the difference but I will look into it.

After reading more up on it, I was thinking maybe accounting for
gradual cutoffs near the ends using rcoulomb_switch and similarly for
rvdw.

Anything wrong with the way I created the topology?  Dr. Vitaly, I
also attached the *.itp files like you mentioned.

Thanks again for all your help.



On Mon, May 2, 2011 at 2:16 PM, Fabian Casteblanco
 wrote:
> Hello,
>
> I have been trying to use CHARMM forcefield to simulate 1000 molecules
> of Methanol in a box but I seem to fall short on the density every
> time I run.  At first, I had my rlist at 1 but CHARMM recommends
> greater than 1.2-1.4 nm so I changed accordingly, then I changed it so
> that the short neighbor list would update more freqently and finally I
> even added a greater amount of steps, hoping that the pressure and
> density would settle down at some value.
>
> Below, I had taken and modified from the Lysozyme tutorial.  One thing
> I noticed is the contraint -algorithm and how the constraints are set
> to 'all-bonds'.  Is this necessary?  After running NVT (leveled off
> near 298K, seemed ok), then NPT, for 300,000 steps, the pressure is
> close to the reference 1 bar, ~1.1,1.2 bar, but I noticed the density
> is still oscillating, not by much, but it still leaves me questioning
> why its not settling around to the literature value of 0.791 g/cm3.  I
> posted the last several lines from the analysis *.xvg file.  NPT
> script is also below.
>
> Is there still more steps that I have to run for?  The density just
> seems to be oscillating too much and although a literature value of
> 0.791 g/cm3 is within the data, it doesnt seem to be settling around
> that value.  I have similar problems for 1-propanol to where my
> simulated density is under that of the literature value.  Could it be
> possible that maybe I should use different NVT, NPT algorithms
> (tcoupl, pcoupl)?
>
> I would really appreciate anyones help. I'm still in my first few
> months of learning the program.  Thanks!
>
>  591.80  38039.125000  297.409546  -206.071747  779.428894
>  592.00  38035.421875  294.95  -20.557419  777.816956
>  592.20  37982.812500  298.063324  -463.192047  776.430542
>  592.40  37681.421875  295.430878   36.529854  776.460876
>  592.60  37476.148438  297.193787  -28.961288  775.634644
>  592.80  37611.574219  297.059875  -553.369263  774.096924
>  593.00  37682.277344  288.297974  -293.567963  776.055237
>  593.20  37147.824219  295.985901  -221.989441  781.570679
>  593.40  37404.906250  293.938721  399.093018  788.921570
>  593.60  37339.914062  297.464783  415.891235  793.838440
>  593.80  37909.019531  292.707184  574.818726  796.730286
>  594.00  37369.820312  304.095703  -119.569496  796.235962
>  594.20  37293.445312  294.449005  -63.335049  794.578552
>  594.40  37196.917969  295.323761  104.148239  791.275085
>  594.60  37776.199219  298.004333   28.989655  785.244629
>  594.80  37893.097656  302.397308  -268.065765  779.457886
>  595.00  38123.460938  295.343109  -140.914047  775.682678
>  595.20  38002.054688  302.233124  -91.893478  774.813660
>  595.40  37835.652344  297.808319  441.931885  776.1420

[gmx-users] Re: ionic liquids

[Vitaly Chaban]

Where are your LJ parameters?

Are you sure that Tsuzuki uses all standard OPLS parameters?

What density do you get in your simulation?


-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216




On Mon, May 2, 2011 at 1:59 AM, Prema Awati  wrote:

>  sir,
>   I am grateful regarding your reply. The reported density for
> [bmim][bf4] system is 1.198 g/cm3.I was wondering whether you asked for the
> topology that I am using for my calculation or the one that
> Tsuzuki.et.al.(one I am referring) have used. Well, following is the
> toopology  that I have created for my system.
>
>
> ;   File 'bmim.top' was generated
> ;   By user: onbekend (0)
> ;   On host: onbekend
> ;   At date: Fri Apr 15 18:03:14 2011
> ;
> ;   This is a include topology file
> ;
> ;   It was generated using program:
> ;   Generated by x2top
> ;
> ;   Command line was:
> ;   g_x2top_d -f boxbmim.pdb -o bmim.top
> ;
> ;   Force field was read from the standard Gromacs share directory.
> ;
>
> ; Include forcefield parameters
> #include "oplsaa.ff/forcefield.itp"
>
> [ moleculetype ]
> ; Namenrexcl
> BIM 3
>
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr charge   mass
> typeBchargeB  massB
>  1   opls_557  1BIM NA  1   0.2414.0067   ;
> qtot 0.24
>  2   opls_560  1BIM CW  2  -0.1612.011;
> qtot 0.74
>  3   opls_561  1BIM CW  3  -0.2712.011;
> qtot 1.24
>  4   opls_557  1BIM NA  4   0.3214.0067   ;
> qtot 1.48
>  5   opls_558  1BIM CR  5  -0.2212.011;
> qtot 1.26
>  6   opls_905  1BIM C1  6  -0.3512.011;
> qtot 0.91
>  7   opls_908  1BIM C1  7  -0.1412.011;
> qtot 0.77
>  8   opls_136  1BIM C2  8  -0.1212.011;
> qtot 0.65
>  9   opls_136  1BIM CS  9  -0.1212.011;
> qtot 0.53
> 10   opls_135  1BIM CT  10 -0.1812.011;
> qtot 0.35
> 11   opls_565  1BIM HA  2   0.23 1.008;
> qtot 0.41
> 12   opls_564  1BIM HA  3   0.27 1.008;
> qtot 0.47
> 13   opls_563  1BIM HA  5   0.25 1.008;
> qtot 0.53
> 14   opls_911  1BIM H1  6   0.17 1.008;
> qtot 0.59
> 15   opls_911  1BIM H1  6   0.17 1.008;
> qtot 0.65
> 16   opls_911  1BIM H1  6   0.17 1.008;
> qtot 0.71
> 17   opls_911  1BIM H1  7   0.16 1.008;
> qtot 0.77
> 18   opls_911  1BIM H1  7   0.16 1.008;
> qtot 0.83
> 19   opls_140  1BIM HC  8   0.06 1.008;
> qtot 0.89
> 20   opls_140  1BIM HC  8   0.06 1.008;
> qtot 0.95
> 21   opls_140  1BIM HC  9   0.06 1.008;
> qtot 1.01
> 22   opls_140  1BIM HC  9   0.06 1.008;
> qtot 1.07
> 23   opls_140  1BIM HC  10  0.06 1.008;
> qtot 1.13
> 24   opls_140  1BIM HC  10  0.06 1.008;
> qtot 1.19
> 25   opls_140  1BIM HC  10  0.06 1.008;
> qtot 1.25
>
> [ bonds ]
> ;  aiaj functc0c1c2c3
> 1 2 1  0.1372   178656.8
> 1 5 1  0.1340   199576.8
> 1 6 1  0.1466   141000.8
> 2 3 1  0.1375   217568.0
> 211 1  0.1080   138490.4
> 3 4 1  0.1372   178656.8
> 312 1  0.1080   138490.4
> 4 5 1  0.1340   199576.8
> 4 7 1  0.1466   141000.8
> 513 1  0.1080   138490.4
> 614 1  0.1090   138490.4
> 615 1  0.1090   138490.4
> 616 1  0.1090   138490.4
> 7 8 1  0.1516   112131.2
> 717 1  0.1090   138490.4
> 718 1  0.1090   138490.4
> 8 9 1  0.1529   112131.2
> 819 1  0.1090   138490.4
> 820 1  0.1090   138490.4
> 910 1  0.1529   112131.2
> 921 1  0.1090   138490.4
> 922 1  0.1090   138490.4
>1023 1  0.1090   138490.4
>1024 1  0.1090   138490.4
>1025 1  0.1090   138490.4
>
> [ pairs ]
> ;  aiaj functc0c1c2c3
> 1 7 1
> 112 1
> 2 7 1
> 213 1
> 214 1
> 215 1
> 216 1
> 3 6 1
> 3 8 1
> 313 1
> 317 1
> 318 1
> 4 6 1
> 4 9 1
> 411 1
> 419 1
> 420 1
> 5 8 1
> 

[gmx-users] Re: Unsteady Density

[Vitaly Chaban]

>
>
> I have been trying to use CHARMM forcefield to simulate 1000 molecules
> of Methanol in a box but I seem to fall short on the density every
> time I run.  At first, I had my rlist at 1 but CHARMM recommends
> greater than 1.2-1.4 nm so I changed accordingly, then I changed it so
> that the short neighbor list would update more freqently and finally I
> even added a greater amount of steps, hoping that the pressure and
> density would settle down at some value.
>
> Below, I had taken and modified from the Lysozyme tutorial.  One thing
> I noticed is the contraint -algorithm and how the constraints are set
> to 'all-bonds'.  Is this necessary?  After running NVT (leveled off
> near 298K, seemed ok), then NPT, for 300,000 steps, the pressure is
> close to the reference 1 bar, ~1.1,1.2 bar, but I noticed the density
> is still oscillating, not by much, but it still leaves me questioning
> why its not settling around to the literature value of 0.791 g/cm3.  I
> posted the last several lines from the analysis *.xvg file.  NPT
> script is also below.
>
> Is there still more steps that I have to run for?  The density just
> seems to be oscillating too much and although a literature value of
> 0.791 g/cm3 is within the data, it doesnt seem to be settling around
> that value.  I have similar problems for 1-propanol to where my
> simulated density is under that of the literature value.  Could it be
> possible that maybe I should use different NVT, NPT algorithms
> (tcoupl, pcoupl)?
>
> I would really appreciate anyones help. I'm still in my first few
> months of learning the program.  Thanks!
>
>  591.80  38039.125000  297.409546  -206.071747  779.428894
>  592.00  38035.421875  294.95  -20.557419  777.816956
>  592.20  37982.812500  298.063324  -463.192047  776.430542
>  592.40  37681.421875  295.430878   36.529854  776.460876
>  592.60  37476.148438  297.193787  -28.961288  775.634644
>  592.80  37611.574219  297.059875  -553.369263  774.096924
>  593.00  37682.277344  288.297974  -293.567963  776.055237
>  593.20  37147.824219  295.985901  -221.989441  781.570679
>  593.40  37404.906250  293.938721  399.093018  788.921570
>  593.60  37339.914062  297.464783  415.891235  793.838440
>  593.80  37909.019531  292.707184  574.818726  796.730286
>  594.00  37369.820312  304.095703  -119.569496  796.235962
>  594.20  37293.445312  294.449005  -63.335049  794.578552
>  594.40  37196.917969  295.323761  104.148239  791.275085
>  594.60  37776.199219  298.004333   28.989655  785.244629
>  594.80  37893.097656  302.397308  -268.065765  779.457886
>  595.00  38123.460938  295.343109  -140.914047  775.682678
>  595.20  38002.054688  302.233124  -91.893478  774.813660
>  595.40  37835.652344  297.808319  441.931885  776.142090
>  595.60  38103.964844  296.369019  490.766754  778.422302
>  595.80  37686.902344  303.358093  -19.726471  781.057922
>  596.00  37586.890625  293.751648  -92.387199  783.724854
>  596.20  37408.414062  300.007385  -288.156036  785.990417
>  596.40  37894.898438  295.720520  346.861206  788.753174
>  596.60  37673.378906  288.311432   89.059952  789.179993
>  596.80  36881.062500  295.265564   70.789131  791.552673
>  597.00  37077.789062  296.261444   72.207787  793.970398
>  597.20  37123.230469  296.511475  -232.434616  793.653564
>  597.40  37426.152344  304.281891  -133.300797  791.791077
>  597.60  37514.332031  305.183197  -259.364136  787.592712
>  597.80  37393.667969  301.326111  -150.162338  785.053711
>  598.00  37263.054688  299.811554  326.851837  785.553894
>  598.20  37203.261719  300.688904  225.526001  788.008667
>  598.40  37511.636719  302.506714   66.299194  790.725281
>  598.60  37460.843750  299.512909  198.943665  793.35
>  598.80  37248.921875  291.575134  -93.283127  793.582703
>  599.00  36870.480469  293.515381  211.069107  792.929443
>  599.20  37398.097656  293.184448  -163.371140  789.150513
>  599.40  37402.238281  297.402008   45.650658  786.303711
>  599.60  37419.816406  298.520508  -147.688004  783.492371
>  599.80  37497.332031  296.529877  -15.991615  782.294250
>  600.00  37691.468750  298.839844  -68.580627  781.974182
>
>
>
> title   =Methanol npt equilibration
>
> ;Run parameters
> integrator  =md ;leap-frog algorithm
> nsteps  =30 ;2 * 5 = 100 ps
> dt  =0.002  ;2fs
>
> ;Output control
> nstxout =100;save coordinates every 0.2 ps
> nstvout =100;save velocities every 0.2 ps
> nstenergy   =100;save energies every 0.2 ps
> nstlog  =100;update log file every 0.2 ps
>
> ;Bond parameters
> continuation =yes   ;Restarting after NVT
> constraint_algorithm=lincs  ;holonomic constraints
> constraints 

Re: [gmx-users] Unsteady Density

[Justin A. Lemkul]

Fabian Casteblanco wrote:

Hello,

I have been trying to use CHARMM forcefield to simulate 1000 molecules
of Methanol in a box but I seem to fall short on the density every
time I run.  At first, I had my rlist at 1 but CHARMM recommends
greater than 1.2-1.4 nm so I changed accordingly, then I changed it so
that the short neighbor list would update more freqently and finally I
even added a greater amount of steps, hoping that the pressure and
density would settle down at some value.



nstlist = 1 is probably overkill.  Such frequent updating should only be 
necessary for EM.



Below, I had taken and modified from the Lysozyme tutorial.  One thing
I noticed is the contraint -algorithm and how the constraints are set
to 'all-bonds'.  Is this necessary?  After running NVT (leveled off


Contraints should be applied unless you want your timestep to be limited to 
0.5-1 fs.  Being that you're using a 2-fs timestep, yes, constraints are 
necessary.  There is a discussion about all of this in the manual and in the 
LINCS papers.



near 298K, seemed ok), then NPT, for 300,000 steps, the pressure is
close to the reference 1 bar, ~1.1,1.2 bar, but I noticed the density
is still oscillating, not by much, but it still leaves me questioning
why its not settling around to the literature value of 0.791 g/cm3.  I


How far off from the literature value is your result?


posted the last several lines from the analysis *.xvg file.  NPT
script is also below.


The posted data are meaningless without labels to know what we're looking at. 
Raw output from .xvg files is usually not useful.  Averages and fluctuations 
printed from .edr files, however, is more useful, since it is accurate over all 
MD steps, whereas the resulting .xvg files contain only frames corresponding to 
nstenergy intervals.




Is there still more steps that I have to run for?  The density just
seems to be oscillating too much and although a literature value of
0.791 g/cm3 is within the data, it doesnt seem to be settling around
that value.  I have similar problems for 1-propanol to where my
simulated density is under that of the literature value.  Could it be
possible that maybe I should use different NVT, NPT algorithms
(tcoupl, pcoupl)?



Your settings should correspond to an accurate ensemble, but I suppose you could 
mess around with them.  Berendsen should be avoided.


The one factor you've not really mentioned is your topology.  One of the most 
important factors in determining the accuracy of your simulation is the 
parameters assigned to the actual molecules.  How did you derive the topologies? 
 Are the parameters used (charges, atom types, etc) consistent with any 
literature precedent?



compressibility =4.5e-5 ;isothermal compressibility of h2O, 
1/bar


Note that you're using the compressibility for water rather than your actual 
systems.  This could explain some discrepancy.


-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] Unsteady Density

[Fabian Casteblanco]

Hello,

I have been trying to use CHARMM forcefield to simulate 1000 molecules
of Methanol in a box but I seem to fall short on the density every
time I run.  At first, I had my rlist at 1 but CHARMM recommends
greater than 1.2-1.4 nm so I changed accordingly, then I changed it so
that the short neighbor list would update more freqently and finally I
even added a greater amount of steps, hoping that the pressure and
density would settle down at some value.

Below, I had taken and modified from the Lysozyme tutorial.  One thing
I noticed is the contraint -algorithm and how the constraints are set
to 'all-bonds'.  Is this necessary?  After running NVT (leveled off
near 298K, seemed ok), then NPT, for 300,000 steps, the pressure is
close to the reference 1 bar, ~1.1,1.2 bar, but I noticed the density
is still oscillating, not by much, but it still leaves me questioning
why its not settling around to the literature value of 0.791 g/cm3.  I
posted the last several lines from the analysis *.xvg file.  NPT
script is also below.

Is there still more steps that I have to run for?  The density just
seems to be oscillating too much and although a literature value of
0.791 g/cm3 is within the data, it doesnt seem to be settling around
that value.  I have similar problems for 1-propanol to where my
simulated density is under that of the literature value.  Could it be
possible that maybe I should use different NVT, NPT algorithms
(tcoupl, pcoupl)?

I would really appreciate anyones help. I'm still in my first few
months of learning the program.  Thanks!

  591.80  38039.125000  297.409546  -206.071747  779.428894
  592.00  38035.421875  294.95  -20.557419  777.816956
  592.20  37982.812500  298.063324  -463.192047  776.430542
  592.40  37681.421875  295.430878   36.529854  776.460876
  592.60  37476.148438  297.193787  -28.961288  775.634644
  592.80  37611.574219  297.059875  -553.369263  774.096924
  593.00  37682.277344  288.297974  -293.567963  776.055237
  593.20  37147.824219  295.985901  -221.989441  781.570679
  593.40  37404.906250  293.938721  399.093018  788.921570
  593.60  37339.914062  297.464783  415.891235  793.838440
  593.80  37909.019531  292.707184  574.818726  796.730286
  594.00  37369.820312  304.095703  -119.569496  796.235962
  594.20  37293.445312  294.449005  -63.335049  794.578552
  594.40  37196.917969  295.323761  104.148239  791.275085
  594.60  37776.199219  298.004333   28.989655  785.244629
  594.80  37893.097656  302.397308  -268.065765  779.457886
  595.00  38123.460938  295.343109  -140.914047  775.682678
  595.20  38002.054688  302.233124  -91.893478  774.813660
  595.40  37835.652344  297.808319  441.931885  776.142090
  595.60  38103.964844  296.369019  490.766754  778.422302
  595.80  37686.902344  303.358093  -19.726471  781.057922
  596.00  37586.890625  293.751648  -92.387199  783.724854
  596.20  37408.414062  300.007385  -288.156036  785.990417
  596.40  37894.898438  295.720520  346.861206  788.753174
  596.60  37673.378906  288.311432   89.059952  789.179993
  596.80  36881.062500  295.265564   70.789131  791.552673
  597.00  37077.789062  296.261444   72.207787  793.970398
  597.20  37123.230469  296.511475  -232.434616  793.653564
  597.40  37426.152344  304.281891  -133.300797  791.791077
  597.60  37514.332031  305.183197  -259.364136  787.592712
  597.80  37393.667969  301.326111  -150.162338  785.053711
  598.00  37263.054688  299.811554  326.851837  785.553894
  598.20  37203.261719  300.688904  225.526001  788.008667
  598.40  37511.636719  302.506714   66.299194  790.725281
  598.60  37460.843750  299.512909  198.943665  793.35
  598.80  37248.921875  291.575134  -93.283127  793.582703
  599.00  36870.480469  293.515381  211.069107  792.929443
  599.20  37398.097656  293.184448  -163.371140  789.150513
  599.40  37402.238281  297.402008   45.650658  786.303711
  599.60  37419.816406  298.520508  -147.688004  783.492371
  599.80  37497.332031  296.529877  -15.991615  782.294250
  600.00  37691.468750  298.839844  -68.580627  781.974182



title   =Methanol npt equilibration

;Run parameters
integrator  =md ;leap-frog algorithm
nsteps  =30 ;2 * 5 = 100 ps
dt  =0.002  ;2fs

;Output control
nstxout =100;save coordinates every 0.2 ps
nstvout =100;save velocities every 0.2 ps
nstenergy   =100;save energies every 0.2 ps
nstlog  =100;update log file every 0.2 ps

;Bond parameters
continuation =yes   ;Restarting after NVT
constraint_algorithm=lincs  ;holonomic constraints
constraints  =all-bonds ;all bonds (even heavy atom-H
bonds)constraind
lincs_iter   =1 ;accuracy of LINCS
linc

Re: [gmx-users] Re: [gmx-developers] installing the parallel version of Gromacs 3.3.1

[Alexey Shvetsov]

Hi all!

There also another problem. You are using intel compilers on amd based 
machine. Intel compilers uses cpuid to identify processor and optimization and 
they doesnt include amd cpuids at all. So you will have bad performance on amd 
cpus. I'd recomend to use recent versions of gcc (gcc-4.5+) and math libs like 
atlas or gotoblas2 for blas and lapack. This combination will perform much 
better then icc

On 2 of May 2011 10:56:19 Justin A. Lemkul wrote:
> I am CC'ing this message to the general gmx-users list.  The gmx-developers
> list is for discussion about development.  Please send anything further via
> gmx-users.
> 
> See comments below.
> 
> West, Ana wrote:
> > Dear Gromacs Community,
> > 
> > I attempted to install the parallel version of Gromacs 3.3.1 on a
> > machine with the x86-64 architecture and 8 core AMD Opteron processors.
> > The operating system is openSusie 11.3. During my attempt I used the
> > following set of commands:
> > 
> > ./configure --prefix=/usr/local/packages/gromacs-3.3.1
> > --enable-mpi CC=icc CXX=icpc F77=ifort
> > make mdrun
> > make mdrun install
> > 
> > The version of the three compilers is 12.0.3. The installation seemed
> > unsuccessful. In the 'config.log' file the fatal error message reads as
> > :
> > 
> > "Fatal Error: This program was not built to run on the processor in your
> > system. The allowed processors are: Intel(R) Pentium(R) 4 and compatible
> > Intel processors with Intel(R) Streaming SIMD Extensions 3 (Intel(R)
> > SSE3) instruction support."
> > 
> > Could someone please provide me with some kind advice?
> 
> Your hardware is too new to install the (archaic!) version of Gromacs you're
> trying to use.  I suspect you would have more success with a version of
> Gromacs that is not five years old.
> 
> Either use a newer version of Gromacs, or find a slower machine.
> 
> -Justin
> 
> > Thank you,
> > Ana

-- 
Best Regards,
 Alexey 'Alexxy' Shvetsov
 Petersburg Nuclear Physics Institute, Russia
 Department of Molecular and Radiation Biophysics
 Gentoo Team Ru
 Gentoo Linux Dev
 mailto:alexx...@gmail.com
 mailto:ale...@gentoo.org
 mailto:ale...@omrb.pnpi.spb.ru

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[gmx-users] Re: mixtures. I want to build my simulation box as tutorial

[Vitaly Chaban]

>
>
> Hi
>
> I want to build my simulation box as tutorial. However I change
> "vdwradii.dat" file according to the tutorial liquid 2 mix with liquid 1.
> What should I do?
>


Your question is not clear.


-- 
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University of Rochester, Rochester, New York 14627-0216
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Re: [gmx-users] adding to liquids in the simulation box: one is in the right side of the box and the other in the left side

[Justin A. Lemkul]

Please do not reply to the entire digest.  Parse any relevant text, choose an 
appropriate subject line, and reply.  Otherwise, the archive gets hopelessly 
confused.


Maria Hamilton wrote:

Hi

I want to build my simulation box as tutorial. However I change 
"vdwradii.dat" file according to the tutorial liquid 2 mix with liquid 
1. What should I do?




So increase the radius of whatever atom types are needed until the solvents 
don't mix.  The tutorial provides a generic workflow for a discrete system; you 
may have to tweak it to suit your needs.


-Justin


Thanks

Maria


--


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] Re: adding to liquids in the simulation box: one is in the right side of the box and the other in the left side

[Vitaly Chaban]

On Mon, May 2, 2011 at 11:55 AM, Maria Hamilton
wrote:

> 1.Does any liquid have an individual "vdwradii.dat"?
>

"vdwradii.dat" is one for all atoms. It is in the same directory with
built-in topologies. The atom names in your conf.gro and this "vdwradii.dat"
should coincide, while genbox is operating.



> I found only one "vdwradii.dat" file in GROMACS folder.
> 2.How can I freeze the first liquid?
>


Use *freeze groups* and *freeze dimensions* keywords. See reference for
parameters in MDP to get exact names of them.


-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216




> On Mon, May 2, 2011 at 6:10 PM, Vitaly Chaban  wrote:
>
>> To do this at first I fill my box using "genbox" with one of the liquids
>>> as
>>> solvent: I used -cs and I did not used -cp.
>>> and then I used "genbox" again to add the other liquid in it: first
>>> liquid
>>> as a solute and the second one is as solvent. But these two liquids gives
>>> me
>>> a solution. I want to preovent mixing of them. what should I do?
>>>
>>
>>
>> 1. Create a box.
>> 2. Add the first liquid as usually (using genbox).
>> 3. Equilibrate a system.
>> 4. Enlarge your box in certain direction, i.e. manually change the side
>> length in GRO file.
>> 5. Add the second liquid (using genbox). To ensure that molecules of the
>> second type are unable to fit to the voids between the molecules of the
>> first type, you may somewhat enlarge VDW radius for certain site of molecule
>> # 2 in the "vdwradii.dat" file.
>> 6. Freeze molecules # 1 and equilibrate the subsystem with molecules # 2.
>>
>>
>> --
>> Dr. Vitaly V. Chaban, Department of Chemistry
>> University of Rochester, Rochester, New York 14627-0216
>>
>
>
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[gmx-users] g_traj -ox -com slight inconsistency

[Chris Neale]

Dear Users:

I have noticed an inconsistency with g_traj -ox -com output when using 
-f a.gro and either -s a.gro or -s a.tpr where a.tpr was constructed 
from a.gro.


There does not appear to be any difference when not using the -com flag.

The difference is on the order of <=0.008 nm so I suppose that it could 
be related to rounding and order of operations or precision.


The same results exist for at least 4.0.5 and 4.5.3.

Thanks,
Chris.
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[gmx-users] Re: gmx-users Digest, Vol 85, Issue 9

[Maria Hamilton]

t; >>
> >>This is a meaningless comment.  It was left there from copying and
> >>pasting files before modifying them.  The important part is that
> >>"continuation = yes" be set to correctly solve the constraints.
> >>
> >>
> >>we run a NPT and then Pulling, then extracted some
> >>configurations from pull.trr file.
> >>I think we must continue from pull.cptnot   NPT.cpt
> >>
> >>I mean :
> >>grompp   -f  md_umbrella.mdp .  -t
> >>  pull.cpt  is more correct than
> >>
> >>grompp-f md_umbrella.mdp .. -t
> >> NPT.cpt
> >>
> >>am I right?
> >>
> >>
> >>In the case of the tutorial, no.  There is not a corresponding .cpt
> >>file for each configuration generated.  If you were to somehow apply
> >>the same .cpt file for each configuration, almost certainly some of
> >>the windows would blow up because the initial velocities would cause
> >>nasty collisions.  Note that I discuss the continuation issue,
> >>proper settings for gen_vel, etc. in the tutorial, step six.
> >>
> >>-Justin
> >>
> >>
> >>Thanks in advance for your reply
> >>
> >>
> >>-- 
> >>
> >>Justin A. Lemkul
> >>Ph.D. Candidate
> >>ICTAS Doctoral Scholar
> >>MILES-IGERT Trainee
> >>Department of Biochemistry
> >>Virginia Tech
> >>Blacksburg, VA
> >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> >>
> >>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>
> >>
> >>-- gmx-users mailing listgmx-users@gromacs.org
> >><mailto:gmx-users@gromacs.org>
> >>
> >>http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>Please search the archive at
> >>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>Please don't post (un)subscribe requests to the list. Use the www
> >>interface or send it to gmx-users-requ...@gromacs.org
> >><mailto:gmx-users-requ...@gromacs.org>.
> >>
> >>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >>
> >>
> > --
> > 
> >
> > 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
> >
> > 
> > --
> > 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
> >
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110502/25076a8a/attachment-0001.html
>
> --
>
> Message: 2
> Date: Mon, 2 May 2011 17:19:00 +0430
> From: Maria Hamilton 
> Subject: [gmx-users] adding an identified number of water molecules
> To: gmx-users@gromacs.org
> Message-ID: 
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi all
>
> If I want to add a simulation box an identified number of water molecules
> what should I do?
> In manual I see -nmol and -ci in genbox for insert extra molecules but I
> don't know for solvent what should I do?
>
> Thanks alot
>
> Best Regards
>
> Maria
> -- next part --
> An HTML attachment was scrubbed...
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> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110502/f486c0c6/attachment-0001.html
>
> --
>
> Message: 3
> Date: Mon, 02 May 2011 08:51:51 -0400
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] adding an identified number of water
>m

[gmx-users] Fw: Fw: ionic liquids

[Prema Awati]

 








-- Original Message --

From: prem...@iiserpune.ac.in

To: gmx-users@gromacs.org

Date: Mon, 2 May 2011 12:06:34 +0530 (GMT+05:30)

Subject: Fw: ionic liquids













-- Original 
Message --

From: 
prem...@iiserpune.ac.in

To: 
vvcha...@gmail.com

Date: Mon, 2 
May 2011 11:29:44 +0530 (GMT+05:30)

Subject: ionic 
liquids



sir,

I am grateful 
regarding your reply. The reported density for [bmim][bf4] system is 1.198 
g/cm3.I was wondering whether you asked for the topology that I am using for my 
calculation or the one that Tsuzuki.et.al.(one I am referring) have used. Well, 
following is the toopology that I have created for my system.





; File 
'bmim.top' was generated

; By user: 
onbekend (0)

; On host: 
onbekend

; At date: Fri 
Apr 15 18:03:14 2011

;

; This is a 
include topology file

;

; It was 
generated using program:

; Generated by 
x2top

;

; Command line 
was:

; g_x2top_d -f 
boxbmim.pdb -o bmim.top

;

; Force field 
was read from the standard Gromacs share directory.

;



; Include 
forcefield parameters

#include 
"oplsaa.ff/forcefield.itp"



[ moleculetype ]

; Name nrexcl

BIM 3



[ atoms ]

; nr type resnr 
residue atom cgnr charge mass typeB chargeB massB

1 opls_557 1 
BIM NA 1 0.24 14.0067 ; qtot 0.24

2 opls_560 1 
BIM CW 2 -0.16 12.011 ; qtot 0.74

3 opls_561 1 
BIM CW 3 -0.27 12.011 ; qtot 1.24

4 opls_557 1 
BIM NA 4 0.32 14.0067 ; qtot 1.48

5 opls_558 1 
BIM CR 5 -0.22 12.011 ; qtot 1.26

6 opls_905 1 
BIM C1 6 -0.35 12.011 ; qtot 0.91

7 opls_908 1 
BIM C1 7 -0.14 12.011 ; qtot 0.77

8 opls_136 1 
BIM C2 8 -0.12 12.011 ; qtot 0.65

 

[gmx-users] Re: adding to liquids in the simulation box: one is in the right side of the box and the other in the left side

[Maria Hamilton]

1.Does any liquid have an individual "vdwradii.dat"?
I found only one "vdwradii.dat" file in GROMACS folder.
2.How can I freeze the first liquid?

Thanks

Regards

Maria
On Mon, May 2, 2011 at 6:10 PM, Vitaly Chaban  wrote:

> To do this at first I fill my box using "genbox" with one of the liquids as
>> solvent: I used -cs and I did not used -cp.
>> and then I used "genbox" again to add the other liquid in it: first liquid
>> as a solute and the second one is as solvent. But these two liquids gives
>> me
>> a solution. I want to preovent mixing of them. what should I do?
>>
>
>
> 1. Create a box.
> 2. Add the first liquid as usually (using genbox).
> 3. Equilibrate a system.
> 4. Enlarge your box in certain direction, i.e. manually change the side
> length in GRO file.
> 5. Add the second liquid (using genbox). To ensure that molecules of the
> second type are unable to fit to the voids between the molecules of the
> first type, you may somewhat enlarge VDW radius for certain site of molecule
> # 2 in the "vdwradii.dat" file.
> 6. Freeze molecules # 1 and equilibrate the subsystem with molecules # 2.
>
>
> --
> Dr. Vitaly V. Chaban, Department of Chemistry
> University of Rochester, Rochester, New York 14627-0216
>
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[gmx-users] Re: [gmx-developers] installing the parallel version of Gromacs 3.3.1

[Justin A. Lemkul]

I am CC'ing this message to the general gmx-users list.  The gmx-developers list 
is for discussion about development.  Please send anything further via gmx-users.


See comments below.

West, Ana wrote:

Dear Gromacs Community,

I attempted to install the parallel version of Gromacs 3.3.1 on a 
machine with the x86-64 architecture and 8 core AMD Opteron processors. 
The operating system is openSusie 11.3. During my attempt I used the 
following set of commands:


./configure --prefix=/usr/local/packages/gromacs-3.3.1 
--enable-mpi CC=icc CXX=icpc F77=ifort

make mdrun
make mdrun install

The version of the three compilers is 12.0.3. The installation seemed 
unsuccessful. In the 'config.log' file the fatal error message reads as :


"Fatal Error: This program was not built to run on the processor in your 
system. The allowed processors are: Intel(R) Pentium(R) 4 and compatible 
Intel processors with Intel(R) Streaming SIMD Extensions 3 (Intel(R) 
SSE3) instruction support." 


Could someone please provide me with some kind advice?



Your hardware is too new to install the (archaic!) version of Gromacs you're 
trying to use.  I suspect you would have more success with a version of Gromacs 
that is not five years old.


Either use a newer version of Gromacs, or find a slower machine.

-Justin

Thank you, 
Ana 






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--


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] Re: adding to liquids in the simulation box: one is in the right side of the box and the other in the left side

[Vitaly Chaban]

>
> To do this at first I fill my box using "genbox" with one of the liquids as
> solvent: I used -cs and I did not used -cp.
> and then I used "genbox" again to add the other liquid in it: first liquid
> as a solute and the second one is as solvent. But these two liquids gives
> me
> a solution. I want to prevent mixing of them. what should I do?
>


1. Create a box.
2. Add the first liquid as usually (using genbox).
3. Equilibrate a system.
4. Enlarge your box in certain direction, i.e. manually change the side
length in GRO file.
5. Add the second liquid (using genbox). To ensure that molecules of the
second type are unable to fit to the voids between the molecules of the
first type, you may somewhat enlarge VDW radius for certain site of molecule
# 2 in the "vdwradii.dat" file.
6. Freeze molecules # 1 and equilibrate the subsystem with molecules # 2.


-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
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Re: [gmx-users] adding to liquids in the simulation box: one is in the right side of the box and the other in the left side

[Justin A. Lemkul]

Maria Hamilton wrote:

Hi all


To do this at first I fill my box using "genbox" with one of the liquids 
as solvent: I used -cs and I did not used -cp.
and then I used "genbox" again to add the other liquid in it: first 
liquid as a solute and the second one is as solvent. But these two 
liquids gives me a solution. I want to prevent mixing of them. what 
should I do?




http://www.gromacs.org/Documentation/Tutorials?highlight=tutorials#Heterogeneous_Systems

-Justin


Thanks alot

Regards

Maria



--


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] adding to liquids in the simulation box: one is in the right side of the box and the other in the left side

[Maria Hamilton]

Hi all


To do this at first I fill my box using "genbox" with one of the liquids as
solvent: I used -cs and I did not used -cp.
and then I used "genbox" again to add the other liquid in it: first liquid
as a solute and the second one is as solvent. But these two liquids gives me
a solution. I want to prevent mixing of them. what should I do?

Thanks alot

Regards

Maria
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Re: [gmx-users] adding an identified number of water molecules

[Justin A. Lemkul]

Maria Hamilton wrote:

Hi all

If I want to add a simulation box an identified number of water 
molecules what should I do?
In manual I see -nmol and -ci in genbox for insert extra molecules but I 
don't know for solvent what should I do?




Please read about the -maxsol option.  I think you will find it most 
informative.

-Justin


Thanks alot

Best Regards

Maria



--


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] adding an identified number of water molecules

[Maria Hamilton]

Hi all

If I want to add a simulation box an identified number of water molecules
what should I do?
In manual I see -nmol and -ci in genbox for insert extra molecules but I
don't know for solvent what should I do?

Thanks alot

Best Regards

Maria
-- 
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Re: [gmx-users] Continuation=yes From?

[mohsen ramezanpour]

Thank you for your detailed axplain
I understood completely

On Mon, May 2, 2011 at 4:34 PM, Justin A. Lemkul  wrote:

>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> Thank you for your reply
>> My  is Protein-ligand,It is have the same conditions as tutorial.I did
>> pull ligand in the z direction.
>> Actualy I found your note about gen_vel ,but I didn't any  about
>> Continuation!
>>
>>
> Not that specific keyword, no, but I do address the general principle about
> continuing these simulations via this very discussion about gen_vel.
>
>
>  You are right,But there is another problem:
>> You have not used any-t option   in grompp command (doing umbrella
>> step).
>>
>>
> Correct.  See the discussion on gen_vel that I referenced earlier.
>
>
>  Since we have set Continuation=yes;
>> Can grompp realize from which .cpt (npt.cpt  )  it must  use ?
>>
>>
> grompp does not make any choice about what it should use.  It takes
> whatever input you give it and assembles a run input file.  If you're
> following my procedure (which may or may not necessarily be applicable in
> all cases), then there will NOT be a suitable .cpt file for each starting
> configuration.  These configurations were generated using SMD, and .cpt
> files are not written and saved at every frame so you have a corresponding
> one later.
>
>
>  And my last question:
>> Do I need to any .cpt file ? (Because I have set Continuation=yes)
>>
>>
> Checkpointing and continuation are related, but not identical.  The
> "continuation" keyword deals with whether or not constraints are solved
> before the first integration step.  It otherwise has nothing to do with the
> thermodynamic state of the system, which is contained in the .cpt file.
>
> For your system, as I state in the tutorial, you may want to set "gen_vel =
> yes" in each window (since there is no prior equilibration, which may be a
> problem for some systems, but not the tutorial example).  This would
> eliminate the need for a .cpt file.
>
> -Justin
>
>  Thanks in advance
>>
>>
>>
>>
>>
>> On Mon, May 2, 2011 at 3:27 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>mohsen ramezanpour wrote:
>>
>>Dear Dr.Justin
>>
>>Regarding Umbrella Sampling tutorial:
>>
>>The CONTINUATION option in md_umbrella.mdp is YES,
>>and you have noticed : From NPT
>>
>>I can't understand it's reason correctly!
>>
>>
>>This is a meaningless comment.  It was left there from copying and
>>pasting files before modifying them.  The important part is that
>>"continuation = yes" be set to correctly solve the constraints.
>>
>>
>>we run a NPT and then Pulling, then extracted some
>>configurations from pull.trr file.
>>I think we must continue from pull.cptnot   NPT.cpt
>>
>>I mean :
>>grompp   -f  md_umbrella.mdp .  -t
>>  pull.cpt  is more correct than
>>
>>grompp-f md_umbrella.mdp .. -t
>> NPT.cpt
>>
>>am I right?
>>
>>
>>In the case of the tutorial, no.  There is not a corresponding .cpt
>>file for each configuration generated.  If you were to somehow apply
>>the same .cpt file for each configuration, almost certainly some of
>>the windows would blow up because the initial velocities would cause
>>nasty collisions.  Note that I discuss the continuation issue,
>>proper settings for gen_vel, etc. in the tutorial, step six.
>>
>>-Justin
>>
>>
>>Thanks in advance for your reply
>>
>>
>>-- 
>>
>>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
>>
>>
>>-- 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
>>
>>
>>
> --
> 
>
> 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
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://ww

Re: [gmx-users] Continuation=yes From?

[Justin A. Lemkul]

mohsen ramezanpour wrote:

Dear Dr.Justin

Thank you for your reply
My  is Protein-ligand,It is have the same conditions as tutorial.I did 
pull ligand in the z direction.
Actualy I found your note about gen_vel ,but I didn't any  about 
Continuation!




Not that specific keyword, no, but I do address the general principle about 
continuing these simulations via this very discussion about gen_vel.



You are right,But there is another problem:
You have not used any-t option   in grompp command (doing 
umbrella step).




Correct.  See the discussion on gen_vel that I referenced earlier.


Since we have set Continuation=yes;
Can grompp realize from which .cpt (npt.cpt  )  it must  use ?



grompp does not make any choice about what it should use.  It takes whatever 
input you give it and assembles a run input file.  If you're following my 
procedure (which may or may not necessarily be applicable in all cases), then 
there will NOT be a suitable .cpt file for each starting configuration.  These 
configurations were generated using SMD, and .cpt files are not written and 
saved at every frame so you have a corresponding one later.



And my last question:
Do I need to any .cpt file ? (Because I have set Continuation=yes)



Checkpointing and continuation are related, but not identical.  The 
"continuation" keyword deals with whether or not constraints are solved before 
the first integration step.  It otherwise has nothing to do with the 
thermodynamic state of the system, which is contained in the .cpt file.


For your system, as I state in the tutorial, you may want to set "gen_vel = yes" 
in each window (since there is no prior equilibration, which may be a problem 
for some systems, but not the tutorial example).  This would eliminate the need 
for a .cpt file.


-Justin

Thanks in advance 







On Mon, May 2, 2011 at 3:27 PM, Justin A. Lemkul > wrote:




mohsen ramezanpour wrote:

Dear Dr.Justin

Regarding Umbrella Sampling tutorial:

The CONTINUATION option in md_umbrella.mdp is YES,
and you have noticed : From NPT

I can't understand it's reason correctly!


This is a meaningless comment.  It was left there from copying and
pasting files before modifying them.  The important part is that
"continuation = yes" be set to correctly solve the constraints.


we run a NPT and then Pulling, then extracted some
configurations from pull.trr file.
I think we must continue from pull.cptnot   NPT.cpt

I mean :
grompp   -f  md_umbrella.mdp .  -t  
pull.cpt  is more correct than


grompp-f md_umbrella.mdp .. -t
 NPT.cpt

am I right?


In the case of the tutorial, no.  There is not a corresponding .cpt
file for each configuration generated.  If you were to somehow apply
the same .cpt file for each configuration, almost certainly some of
the windows would blow up because the initial velocities would cause
nasty collisions.  Note that I discuss the continuation issue,
proper settings for gen_vel, etc. in the tutorial, step six.

-Justin


Thanks in advance for your reply


-- 



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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--


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] Adding OPLS-UA forcefield

[Justin A. Lemkul]

Erik Marklund wrote:
I think that it used to be part of earlier (3.?) versions of gmx. Those 
files may be useful for your work.




Presumably, most of OPLS-UA still is.  Per atomtypes.atp, the first 134 opls_* 
types are for OPLS-UA.  I don't know how other features may be impacted, but it 
seems as if the basis for the force field still very much exists.


-Justin


Erik

Zoe Hall skrev 2011-05-02 11.29:

Dear users,

How would I go about adding a united-atom forcefield e.g. OPLS-UA, to 
gromacs 4.5.3?


Thanks in advance,

Zoe

Zoe Hall
Department of Chemistry
Oxford University

zoe.h...@chem.ox.ac.uk










--


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] Adding OPLS-UA forcefield

[Erik Marklund]

I think that it used to be part of earlier (3.?) versions of gmx. Those 
files may be useful for your work.


Erik

Zoe Hall skrev 2011-05-02 11.29:

Dear users,

How would I go about adding a united-atom forcefield e.g. OPLS-UA, to gromacs 
4.5.3?

Thanks in advance,

Zoe

Zoe Hall
Department of Chemistry
Oxford University

zoe.h...@chem.ox.ac.uk








--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] Continuation=yes From?

[mohsen ramezanpour]

Dear Dr.Justin

Thank you for your reply
My  is Protein-ligand,It is have the same conditions as tutorial.I did pull
ligand in the z direction.
Actualy I found your note about gen_vel ,but I didn't any  about
Continuation!

You are right,But there is another problem:
You have not used any-t option   in grompp command (doing umbrella
step).

Since we have set Continuation=yes;
Can grompp realize from which .cpt (npt.cpt  )  it must  use ?

And my last question:
Do I need to any .cpt file ? (Because I have set Continuation=yes)

Thanks in advance






On Mon, May 2, 2011 at 3:27 PM, Justin A. Lemkul  wrote:

>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> Regarding Umbrella Sampling tutorial:
>>
>> The CONTINUATION option in md_umbrella.mdp is YES,
>> and you have noticed : From NPT
>>
>> I can't understand it's reason correctly!
>>
>>
> This is a meaningless comment.  It was left there from copying and pasting
> files before modifying them.  The important part is that "continuation =
> yes" be set to correctly solve the constraints.
>
>
>  we run a NPT and then Pulling, then extracted some configurations from
>> pull.trr file.
>> I think we must continue from pull.cptnot   NPT.cpt
>>
>> I mean :
>> grompp   -f  md_umbrella.mdp .  -t   pull.cpt
>>  is more correct than
>>
>> grompp-f md_umbrella.mdp .. -t  NPT.cpt
>>
>> am I right?
>>
>
> In the case of the tutorial, no.  There is not a corresponding .cpt file
> for each configuration generated.  If you were to somehow apply the same
> .cpt file for each configuration, almost certainly some of the windows would
> blow up because the initial velocities would cause nasty collisions.  Note
> that I discuss the continuation issue, proper settings for gen_vel, etc. in
> the tutorial, step six.
>
> -Justin
>
>
>  Thanks in advance for your reply
>>
>>
> --
> 
>
> 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
>
> 
> --
> 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!
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> or send it to gmx-users-requ...@gromacs.org.
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>
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Re: [gmx-users] Continuation=yes From?

[Justin A. Lemkul]

mohsen ramezanpour wrote:

Dear Dr.Justin

Regarding Umbrella Sampling tutorial:

The CONTINUATION option in md_umbrella.mdp is YES,
and you have noticed : From NPT

I can't understand it's reason correctly!



This is a meaningless comment.  It was left there from copying and pasting files 
before modifying them.  The important part is that "continuation = yes" be set 
to correctly solve the constraints.


we run a NPT and then Pulling, then extracted some configurations from 
pull.trr file.

I think we must continue from pull.cptnot   NPT.cpt

I mean :
grompp   -f  md_umbrella.mdp .  -t   pull.cpt  
is more correct than


grompp-f md_umbrella.mdp .. -t  NPT.cpt

am I right?


In the case of the tutorial, no.  There is not a corresponding .cpt file for 
each configuration generated.  If you were to somehow apply the same .cpt file 
for each configuration, almost certainly some of the windows would blow up 
because the initial velocities would cause nasty collisions.  Note that I 
discuss the continuation issue, proper settings for gen_vel, etc. in the 
tutorial, step six.


-Justin


Thanks in advance for your reply



--


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] reg lincs error and exploding problem during mdrun

[Justin A. Lemkul]

vidhya sankar wrote:

Thanks Justin,
  now i have different problem when i run mdrun_d 
programme with the following command

 ./mdrun_d -s 1HHO_md.tpr -o 1HHO_md.trr  -c 1HHO_md.gro -e md.edr -nt 1
i got error as follows
Step 0, time 0 (ps)  LINCS WARNING


LINCS warnings that occur immediately are almost invariably the result of a poor 
starting configuration.  Better energy minimization and/or equilibration are 
likely necessary.


Another consideration is whether or not these groups:


tc-grps =  HEM   ALOXY; two coupling groups - more accurate


are large enough to justify setting them separately.  Small groups can be 
unstable by themselves.  Hence why one does not, for example, couple ions 
separately from solvent.


-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] Adding OPLS-UA forcefield

[Mark Abraham]

On 02/05/11, Zoe Hall   wrote:
> Dear users,
> 
> How would I go about adding a united-atom forcefield e.g. OPLS-UA, to gromacs 
> 4.5.3? 
> 

Set aside a few weeks, look in share/top/oplsaa.ff, copy it to oplsua.ff in 
your working directory, rework the contents according to the OPLS-UA literature 
and your knowledge of chapter 5 of the GROMACS manual and test the results 
against a suitable reference implementation of OPLS-UA. Good luck!

Mark
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[gmx-users] Adding OPLS-UA forcefield

[Zoe Hall]

Dear users,

How would I go about adding a united-atom forcefield e.g. OPLS-UA, to gromacs 
4.5.3? 

Thanks in advance,

Zoe

Zoe Hall 
Department of Chemistry
Oxford University

zoe.h...@chem.ox.ac.uk





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[gmx-users] Re: polarizable water models

[Ivan Gladich]

Dear Saly
  I am sorry but I am not able to help you on this because I do not 
have any experience with PRODRG and SDS surfactants.


You can try to find something in literature but I have the impression 
that nobody has tested SDS with these water models.

As I told you in the previous mail these water models are quite recent.
You have to test the behaviour of your SDS in these water model using 
some experimental target (e.g. diffusivity, free energy of solvation or 
other...) and see if the force field is reasonable.

Good luck
Ivan


On 04/30/2011 07:21 AM, saly jackson wrote:


Hi Ivan
If in my system there are some of the other components such
SDS surfactant and one of these polarizable models can I use 
forcefield parameters from PRODRG or not.
If no, would you please tell me about the references that I can find 
some other components in polarizable water model

 force fields.
Thanks alot for your help
Regards
Saly
On Wed, Apr 27, 2011 at 5:29 PM, > wrote:


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Today's Topics:

  1. Re: polarizable water models (Mark Abraham)
  2. Re: polarizable water models (Ivan Gladich)


--

Message: 1
Date: Wed, 27 Apr 2011 22:39:56 +1000
From: Mark Abraham mailto:mark.abra...@anu.edu.au>>
Subject: Re: [gmx-users] polarizable water models
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID: <4db80e9c.7010...@anu.edu.au
>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 4/27/2011 10:08 PM, saly jackson wrote:
> Hi Ivan
>

Please do not reply to whole digests with non-descriptive subject
lines.
It confuses the archives, and alienates people from finding out the
topic of your interest, and thus being bothered to give you free help.
Please leave only the relevant discussion, and use a useful
subject line.

> In which force field can I find the polarizable water models you
said
> in section "b" of your reply

Have you done your own literature searching first? Then you'd already
know what force fields they might have been used with...

Mark





--

Message: 2
Date: Wed, 27 Apr 2011 15:43:27 +0200
From: Ivan Gladich mailto:ivan.glad...@marge.uochb.cas.cz>>
Subject: Re: [gmx-users] polarizable water models
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID: <4db81d7f.70...@marge.uochb.cas.cz
>
Content-Type: text/plain; charset="iso-8859-1"

Skipped content of type multipart/alternative-- next
part --
;
; Topology file for SW
;
; Paul van Maaren and David van der Spoel
; Molecular Dynamics Simulations of Water with Novel Shell Model
Potentials
; J. Phys. Chem. B. 105 (2618-2626), 2001
;
; Force constants for the shell are given by:
;
; k = qs^2/(4 pi eps0 alpha)
; However, in the current version of the itp file and software (3.2+)
; force constants are computed in mdrun, and the input is the
; polarizability in nm^3.
;
; Some data: mu (water) = 1.8546 D ( 0.0386116 e nm)
;1/(4 pi eps0 alpha) = 94513.94
;
; Alpha-X = 1.415   kx = 608069
; Alpha-Y = 1.528   ky = 563101
; Alpha-Z = 1.468   kz = 586116
;
; Alpha   = 1.470   k  = 585318
;
; Bonding parameters from (but without cubic term):
; D. M. Ferguson:
; Parametrization and Evaluation of a Flexible Water Model
; J. Comp. Chem. 16(4), 501-511 (1995)
;
; Possible defines that you can put in your topol.top:
; -DANISOTROPIC Select anisotropic polarizibility (isotropic is
default).
; -DRIGID   Rigid model (flexible is default)
; -DPOSRES  Position restrain oxygen atoms
;

[ defaults ]
LJ  Geometric

[ atomtypes ]
;namemass  charge   ptype   c6  c12
  WO15.99940   0.0 A   0.0 0.0
  WH 1.00800   0.0 A   0.0 0.0
  WS 0.0   0.0 S   0.0 0.0
  WD 0.0   0.0 D   0.0 0.0

[ nonbond_params ]
#ifdef RIGID
#ifdef ANISOTROPIC
WH   

[gmx-users] RE: How to use Inflategro with different lipid types

[Ioannis Beis]

Hello,

I would like to thank Justin and Tom for their kind replies to my  
question! I believe that by having the gromacs manual as a guide I  
would manage to bring the bilayer into physiological size by using  
Justin's advice. However, Tom's advice sounds simpler to implement.  
Unfortunately the size of the pre-equilibrated POPC is too small for  
what I want to do afterwards, but I can make my own POPC using  
editconf, genconf and Inflategro to shrink and equilibrate it first  
and then use the renaming trick.


For beginner users that will consult this thread in the future, I had  
overestimated the value of the coordinate files as starting  
structures... Deleting the last two united atoms from oleoyl will fix  
the hydrocarbon chain length and using a palmitoyl force field will  
take care of turning the double bond into a single one. Renaming the  
three different united atoms' names in the polar heads and eventually  
the names of the whole lipids is like turning ethanolamine into  
choline and vice versa. The initial positions at the crucial points  
will be very improper, but this isn't important since hopefully the  
energy minimization will fix them. This strategy -with a little more  
work- could even be applied for more diverse polar heads as soon as  
one has a force field, just by placing his atoms at very reasonable  
initial positions! Proper topology file is all that matters :).


Thanks again for your ideas!

Yiannis

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