date:20121220

Re: [gmx-users] How to convert coarse-grained to fine-grained

2012-12-20 Thread Kieu Thu Nguyen

But, are there any way using this tool in Gromacs v4.5 ? Since i don't want
to remove version 4.5 and install version 3.3.1

Thank All !
KT


On Fri, Dec 21, 2012 at 6:41 AM, Kieu Thu Nguyen wrote:

> Thank Justin so much ! :-)
> KT
>
>
> On Thu, Dec 20, 2012 at 11:54 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 12/20/12 11:38 AM, Kieu Thu Nguyen wrote:
>>
>>> Dear All,
>>>
>>> I convert cg to fg representation by command lines
>>>
>>>   g_fg2cg -pcg cg.top -pfg fg.top -c cg.gro -n 1 -o fg.grog_fg2cg -pcg
>>>
>>> cg.top -pfg fg.top -c cg.xtc -n 1 -o cg2fg.xtc
>>>
>>> But there is a notice "command not found" in the terminal.
>>> I see this command used in Gromacs v3.3.1
>>> Does it not run in Gromacs v4.5 ?
>>>
>>>
>> g_fg2cg is not an official Gromacs program; it is part of a modified
>> 3.3.1 distribution provided by the MARTINI developers.  Their tutorial
>> describes installing and using the modified version.
>>
>> -Justin
>>
>> --
>> ==**==
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> 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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>
>
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Re: [gmx-users] Reduction of system dimensions

2012-12-20 Thread Tsjerk Wassenaar

Hi James,

It's probably better to put all the molecules in the original box (trjconv
-pbc mol), and then delete all molecules with an atom with z<0 or z>9.7. In
addition, why not use a hexagonal prism to limit the size of your system
further? Saves and additional 14%.

Hope it helps,

Tsjerk

On Fri, Dec 21, 2012 at 8:23 AM, James Starlight wrote:

> Dear Gromacs users!
>
>
> I have a protein embedded in membrane surrounded with 2 uipper and
> lower water leafleates. I decide to decrease number of water in that
> system (in both leafletes) by reducing its size in Z-dimension.
> Firstly I've defined new box vectors of my system via editconf and
> than I've uded genbox to cut water in both upper and lower leaflets
> genbox -cs b2ar_Smaller.gro -box 8.68740 8.41864 9.70145
>
> here 9.70145 is the new size of the Z dim (vs 12.0 in old version.
>
> That produce system with desireble water\lipid ratio but atom order in
> protein was perturbed. How I could fix such problem or reduce system
> size by different methods ?
>
>
> James
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada
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[gmx-users] Re: gmx-users Digest, Vol 104, Issue 94

2012-12-20 Thread 申昊

--
> 
> Message: 3
> Date: Thu, 20 Dec 2012 16:06:33 +0100
> From: Erik Marklund 
> Subject: Re: [gmx-users] using g_analyze for calculating distance
>   autocorrelation functions
> To: Discussion list for GROMACS users 
> Message-ID: 
> Content-Type: text/plain; charset=utf-8
> 
> It is common to subtract the average value of the data. Hence the ACF usually 
> contain negative values.

Thank you for your reply. And, how to average the values of the data? averaged 
over the nearest five or ten points or just skip over them?
As i found in the resulted file, the negative points even reach at -0.6. In 
this case even the averaged data should also contain negative points which can 
not be negtived.

> 20 dec 2012 kl. 14.30 skrev ç³æ:
> 
> > 
> > Dear GROMACS users,
> > 
> > I have been working on calculating distance autocorrelation functions by 
> > using g_analyze.
> > The codes i used was 
> > g_analyze -f dist.xvg -ac autocorr.xvg -temp 300.
> > 'dist.xvg' is about the average distance against simulation time. The two 
> > columns are both positive datas.
> > However, the result show a mixture of positive and negative datas. In my 
> > opinion, the autocorrelation function should be always positive. 
> > 
> > Can anyone help me with that ?
> > 
> > HaoShen
> > -- 
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> 
> ---

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Re: [gmx-users] Re: High density after NPT

2012-12-20 Thread Justin Lemkul




On 12/20/12 2:47 PM, zugunder wrote:

Could it be, say, because of still big conformational changes of the protein?
The size of the system is not that small: the protein is hydrated with 10921
water molecules.



Generally restraints are applied to the solute during equilibration to avoid 
structural changes due to clashes with solvent.  Pressure and density are 
related to box size, so any large change in the protein's conformation would 
probably be very obvious and potentially spurious.



What are the variations of pressure and density that could be tolerated at
this step?



Depends on the algorithm.  Pressure is a fickle metric (see 
http://www.gromacs.org/Documentation/Terminology/Pressure and previous 
discussions on this list).  It is generally advisable to run equilibration using 
weak coupling (i.e. Berendsen) methods, then switch to a more robust thermostat 
and barostat for further equilibration and data collection.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] How to convert coarse-grained to fine-grained

2012-12-20 Thread Kieu Thu Nguyen

Thank Justin so much ! :-)
KT


On Thu, Dec 20, 2012 at 11:54 PM, Justin Lemkul  wrote:

>
>
> On 12/20/12 11:38 AM, Kieu Thu Nguyen wrote:
>
>> Dear All,
>>
>> I convert cg to fg representation by command lines
>>
>>   g_fg2cg -pcg cg.top -pfg fg.top -c cg.gro -n 1 -o fg.grog_fg2cg -pcg
>>
>> cg.top -pfg fg.top -c cg.xtc -n 1 -o cg2fg.xtc
>>
>> But there is a notice "command not found" in the terminal.
>> I see this command used in Gromacs v3.3.1
>> Does it not run in Gromacs v4.5 ?
>>
>>
> g_fg2cg is not an official Gromacs program; it is part of a modified 3.3.1
> distribution provided by the MARTINI developers.  Their tutorial describes
> installing and using the modified version.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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> Support/Mailing_Lists/Searchbefore
>  posting!
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RE: [gmx-users] Energy Minimization/ NpT settling problem

2012-12-20 Thread pcl

A couple of things:

1. Are your cutoffs appropriate for OPLS_AA? Even if you fix any code problems 
and using the wrong cutoffs, your results will not be meaningful...
2. How are you generating your box/filling it with molecules? There are 
indications that your original box is too small, or that there are clashing 
atoms in the original configuration, since with a much bigger box you don't 
seem to have problems except for particles moving too rapidly for domain 
decomposition to handle (perhaps there is a cutoff/coupling problem).
2b: what is atom 13090 and what is in its vicinity?

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of emmanuelle [e.a.y.m...@student.tudelft.nl]
Sent: Thursday, December 20, 2012 2:31 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Energy Minimization/ NpT settling problem

Hi,
I am trying to simulate a system consisting of 1790 molecules of
monoethanolamine (MEA), 203 molecules of CO2 and 18210 molecules of
water. After having generated my box and set the density to 1000g/l
using editconf, I am facing a problem with the energy minimization
step. It does not converge to the tolerence I give (Fmax<500kJ/mol). I
get this message:

Steepest Descents converged to machine precision in 199 steps,
but did not reach the requested Fmax < 500.
Potential Energy  = -9.27407663461033e+05
Maximum force =  2.07667591793109e+06 on atom 13090
Norm of force =  1.06912622245517e+04

Since no problem occurs when I simulate CO2 with water only, I think
the problem comes from MEA for which I apply an OPLS_AA force field. I
tried lots of different initial configurations for MEA, using
structures developed with the Avogadro program and structures from
data bank found on the net. All of them result in the same convergence
problem. I don't think there is an issue in my mdp file as I use it
for other simulations which work well. It is as follow:

title   = Minimization  ; Title of run
define  =-DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 500.0 ; Stop minimization when the maximum
force < 500.0 kJ/mol
emstep  = 0.001  ; Energy step size
nsteps  = 10; Maximum number of (minimization)
steps to perform

; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor
list and long range forces
ns_type = grid  ; Method to determine neighbor list
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list
(short range forces)
coulombtype = PME   ; Treatment of long range
electrostatic interactions
rcoulomb= 1.0   ; long range electrostatic cut-off
rvdw= 1.0   ; long range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)

I also tried another approach: I inserted the molecules in a much more
bigger box and performed the energy minimization of this system with a
very low density. This could converge. Afterwards, I run an npT
simulation with a high pressure (10 bar) such that the box shrinks and
that the system reachs the good density. At that step, the following
error came out:

 Making 1D domain decomposition 12 x 1 x 1
starting mdrun 'CO2 in MEA at 303K'
5000 steps,  5.0 ps.
^Mstep 0imb F  4% ^Mstep 100, remaining runtime:   132 s
step 134: Water molecule starting at atom 24060 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

---
Program mdrun_d, VERSION 4.5.5
Source code file: pme.c, line: 538

Fatal error:
1 particles communicated to PME node 7 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Can someone tell me where I am making any mistake and why is my system
not converging?

Thanks in advance,

Emmanuelle
MSc student -TU Delft



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[gmx-users] Energy Minimization/ NpT settling problem

2012-12-20 Thread emmanuelle

Hi,
I am trying to simulate a system consisting of 1790 molecules of
monoethanolamine (MEA), 203 molecules of CO2 and 18210 molecules of
water. After having generated my box and set the density to 1000g/l
using editconf, I am facing a problem with the energy minimization
step. It does not converge to the tolerence I give (Fmax<500kJ/mol). I
get this message:

Steepest Descents converged to machine precision in 199 steps,
but did not reach the requested Fmax < 500.
Potential Energy  = -9.27407663461033e+05
Maximum force =  2.07667591793109e+06 on atom 13090
Norm of force =  1.06912622245517e+04

Since no problem occurs when I simulate CO2 with water only, I think
the problem comes from MEA for which I apply an OPLS_AA force field. I
tried lots of different initial configurations for MEA, using
structures developed with the Avogadro program and structures from
data bank found on the net. All of them result in the same convergence
problem. I don't think there is an issue in my mdp file as I use it
for other simulations which work well. It is as follow:

title   = Minimization  ; Title of run
define  =-DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 500.0 ; Stop minimization when the maximum
force < 500.0 kJ/mol
emstep  = 0.001  ; Energy step size
nsteps  = 10; Maximum number of (minimization)
steps to perform

; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor
list and long range forces
ns_type = grid  ; Method to determine neighbor list
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list
(short range forces)
coulombtype = PME   ; Treatment of long range
electrostatic interactions
rcoulomb= 1.0   ; long range electrostatic cut-off
rvdw= 1.0   ; long range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)

I also tried another approach: I inserted the molecules in a much more
bigger box and performed the energy minimization of this system with a
very low density. This could converge. Afterwards, I run an npT
simulation with a high pressure (10 bar) such that the box shrinks and
that the system reachs the good density. At that step, the following
error came out:

 Making 1D domain decomposition 12 x 1 x 1
starting mdrun 'CO2 in MEA at 303K'
5000 steps,  5.0 ps.
^Mstep 0imb F  4% ^Mstep 100, remaining runtime:   132 s
step 134: Water molecule starting at atom 24060 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

---
Program mdrun_d, VERSION 4.5.5
Source code file: pme.c, line: 538

Fatal error:
1 particles communicated to PME node 7 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Can someone tell me where I am making any mistake and why is my system
not converging?

Thanks in advance,

Emmanuelle
MSc student -TU Delft



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[gmx-users] Re: High density after NPT

2012-12-20 Thread zugunder

Could it be, say, because of still big conformational changes of the protein?
The size of the system is not that small: the protein is hydrated with 10921
water molecules.

What are the variations of pressure and density that could be tolerated at
this step?

Thank you.



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Re: [gmx-users] How to convert coarse-grained to fine-grained

2012-12-20 Thread Justin Lemkul




On 12/20/12 11:38 AM, Kieu Thu Nguyen wrote:

Dear All,

I convert cg to fg representation by command lines

  g_fg2cg -pcg cg.top -pfg fg.top -c cg.gro -n 1 -o fg.grog_fg2cg -pcg
cg.top -pfg fg.top -c cg.xtc -n 1 -o cg2fg.xtc

But there is a notice "command not found" in the terminal.
I see this command used in Gromacs v3.3.1
Does it not run in Gromacs v4.5 ?



g_fg2cg is not an official Gromacs program; it is part of a modified 3.3.1 
distribution provided by the MARTINI developers.  Their tutorial describes 
installing and using the modified version.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] using g_analyze for calculating distance autocorrelation functions

2012-12-20 Thread Erik Marklund

It is common to subtract the average value of the data. Hence the ACF usually 
contain negative values.

20 dec 2012 kl. 14.30 skrev 申昊:

> 
> Dear GROMACS users,
> 
> I have been working on calculating distance autocorrelation functions by 
> using g_analyze.
> The codes i used was 
> g_analyze -f dist.xvg -ac autocorr.xvg -temp 300.
> 'dist.xvg' is about the average distance against simulation time. The two 
> columns are both positive datas.
> However, the result show a mixture of positive and negative datas. In my 
> opinion, the autocorrelation function should be always positive. 
> 
> Can anyone help me with that ?
> 
> HaoShen
> -- 
> gmx-users mailing listgmx-users@gromacs.org
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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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[gmx-users] using g_analyze for calculating distance autocorrelation functions

2012-12-20 Thread 申昊


Dear GROMACS users,

I have been working on calculating distance autocorrelation functions by using 
g_analyze.
The codes i used was 
g_analyze -f dist.xvg -ac autocorr.xvg -temp 300.
'dist.xvg' is about the average distance against simulation time. The two 
columns are both positive datas.
However, the result show a mixture of positive and negative datas. In my 
opinion, the autocorrelation function should be always positive. 

Can anyone help me with that ?

HaoShen
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Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

2012-12-20 Thread Peter C. Lai

You can always see if you have any by looking at cgnr column of the protein
.itp file. If each atom is in its own chargegroup (the cgnr increments by 
atom) then it's fine.

Is this charmm36 (when did you install this from the website?)or 
27 (what gromacs version)? There were two chargegroup problems fixed in two 
successive versions. First, I think 4.5.4 Charmm27 removed all chargegroups
for by default in the .rtp files. Then, the charmm36 upload was fixed to
do that too. However, I am not sure what versions has fixed terminii. 
In gromacs 4.5.3 and the charmm36 from that time period would generate 
capping groups with a single large chargegroup.

Anyway, Grompp will give you an idea if you have a really large chargegroup 
when it gives you the notice about them; if your largest chargegroup is 
comparable to the van der waals diamater of two atoms I don't think there is 
anything to worry about. If you do have a lot of large chargegroups, 
apparently you might run into cutoff artifacts but I'm not sure exactly.

On 2012-12-20 01:37:25PM +0300, James Starlight wrote:
> Peter,
> 
> what errors might occurs if I've missed -nochargegrp option while
> parametrising  my protein by means of pdb2gmx?
> 
> 
> James
> 
> 
> 2012/12/20 Peter C. Lai :
> > (As a side note, Gromacs shouldn't use charge groups when using
> > all-atom charmm forcefields.)
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[gmx-users] virtual sites with CHARMM lipids

2012-12-20 Thread Bastien Loubet

Dear GROMACS users,

I have been working on a CHARMM36 POPC bilayer and in order to accelerate
the simulation we want to use virtual sites for the hydrogen atoms in the
lipid.

We mainly want to do it for the carbon tails of the lipids.
I have checked the different type of virtual sites in the GROMACS manual
(3fd, 3fda, 3out, N) but none of them seems to correspond to the CH2 groups
in the carbon chains.
It would require an out of plane virtual site with fixed length (so using
normalized vector).

Can you help me with that ?

Thanks,

Bastien Loubet



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Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

2012-12-20 Thread James Starlight

Peter,

what errors might occurs if I've missed -nochargegrp option while
parametrising  my protein by means of pdb2gmx?


James


2012/12/20 Peter C. Lai :
> (As a side note, Gromacs shouldn't use charge groups when using
> all-atom charmm forcefields.)
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Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

2012-12-20 Thread Peter C. Lai

I don't know.

Parachem outputs stuff like this (CHARMM toppar format):

(propionic acid, C3H2O5)

RESI PROA -1.00 
GROUP
ATOM  C2  CG321   -0.28 
ATOM  C1  CG2O30.62 
ATOM  H21 HGA2 0.09 
ATOM  H22 HGA2 0.09   
ATOM  O1  OG2D2   -0.76 
ATOM  O2  OG2D2   -0.76 
GROUP   
ATOM  C3  CG331   -0.27 
ATOM  H31 HGA3 0.09
ATOM  H32 HGA3 0.09
ATOM  H33 HGA3 0.09

BOND C1 C2  C2 C3  C1 O1
BOND C2 H21 C2 H22
BOND C3 H31 C3 H32 C3 H33
DOUBLE  C1 O2
IMPR C1 O2 O1 C2

which you can easily write a script to convert to .rtp (or just convert by
hand) but it'd be more complicated to create an entire .itp from this
format; pdb2gmx will do it if you convert this to .rtp though. I also
frequently encounter ligands that don't have hydrogens too, so that's why
I would write a .hdb entry if necessary.

(As a side note, Gromacs shouldn't use charge groups when using 
all-atom charmm forcefields.)

On 2012-12-20 09:27:12AM +0100, Albert wrote:
> On 12/20/2012 09:13 AM, pcl wrote:
> > Well what works for me is I convert cgenff and merge it with charmm36 (you 
> > only have to do this once per cgenff version), then I have paramchem 
> > generate cgenff charges for the ligand. Then I convert the output of 
> > paramchem (charges) to .rtp format. I also have to create .hdb entries. 
> > Paramchem may also generate additional cgenff atom interactions (dihedrals 
> > or impropers) that may not exist by default, I usually convert and add 
> > those to forcefield's .itp files. Then pdb2gmx will work on the ligand pdb.
> 
> 
> but isn't there is a script to do so in Gromacs webiste, which can 
> convert the output from parachem into Gromacs .itp format? although I 
> didn't try it hard, because I don't find any documentation to use it 
> correctly.
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Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

2012-12-20 Thread Albert


On 12/20/2012 09:13 AM, pcl wrote:

Well what works for me is I convert cgenff and merge it with charmm36 (you only 
have to do this once per cgenff version), then I have paramchem generate cgenff 
charges for the ligand. Then I convert the output of paramchem (charges) to 
.rtp format. I also have to create .hdb entries. Paramchem may also generate 
additional cgenff atom interactions (dihedrals or impropers) that may not exist 
by default, I usually convert and add those to forcefield's .itp files. Then 
pdb2gmx will work on the ligand pdb.



but isn't there is a script to do so in Gromacs webiste, which can 
convert the output from parachem into Gromacs .itp format? although I 
didn't try it hard, because I don't find any documentation to use it 
correctly.

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RE: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

2012-12-20 Thread pcl

Well what works for me is I convert cgenff and merge it with charmm36 (you only 
have to do this once per cgenff version), then I have paramchem generate cgenff 
charges for the ligand. Then I convert the output of paramchem (charges) to 
.rtp format. I also have to create .hdb entries. Paramchem may also generate 
additional cgenff atom interactions (dihedrals or impropers) that may not exist 
by default, I usually convert and add those to forcefield's .itp files. Then 
pdb2gmx will work on the ligand pdb.

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of James Starlight [jmsstarli...@gmail.com]
Sent: Thursday, December 20, 2012 12:48 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

Peter,


so as I understood after the integration of the CGenFF params into the
charm36 rtp ligand ( in complex with the protein) might be
parametrized just by pdb2gmx. Does this correct ?


James

2012/12/20 Peter C. Lai :
> I am not 100% sure how the differences in c36 will affect the parameters you
> get from SwissParam.
>
> Personally I prefer to use ParamChem (CHARMM's version of Swissprot) to
> give me ligand parameters using CGenFF atomtypes, since I have CGenFF
> merged into my Charmm36 forcefield in gromacs.
>
>
> On 2012-12-19 10:37:40AM +0300, James Starlight wrote:
>> Peter, many thanks!
>>
>>
>> Could you tell me is there any differences in atom types between
>> charmm27 and charmm36 ff? I'd like to simulate receptor-ligand complex
>> in that bilayer where ligand molecule would be parametrized by
>> Swiss-param ( make topology for the ligands in charmm27 ff). So
>> because receptor and bilayer will be parametrized in charmm36 I'm not
>> sure about proper working of Swiss's topology with that complex.
>>
>> James
>>
>> 2012/12/19 Peter C. Lai :
>> > http://cesium.hyperfine.info/~peter/gromacs/popc36/
>> > has a fully gromacs compatible charmm36 238 POPC bilayer with 21524 waters
>> >
>> > On 2012-12-18 09:07:22PM -0800, James Starlight wrote:
>> >> Justin, thanks again.
>> >>
>> >> As I understood gromacs already had had parameters for charmm lipid so
>> >> the main approach is to do ITP file for 1 lipid by means of pdb2gmx
>> >> isnt it?
>> >>
>> >> By the way is there any way to convert PSF or CRD file to PDB?
>> >>
>> >> I've found suitable bilayer for my simulation but it lack such 
>> >> coordinates.
>> >> POPE Bilayer (310.15K, A=65.2 Â/lipid, 10ns, 340 lipids, noLRCs):
>> >> CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD
>> >>
>> >> James
>> >>
>> >> 2012/12/18, Justin Lemkul :
>> >> >
>> >> >
>> >> > On 12/18/12 2:02 PM, James Starlight wrote:
>> >> >> Dear Gromacs Users!
>> >> >>
>> >> >> I'm looking for 150-200 lipid bilayer ( POPC or POPE) parametrized in
>> >> >> charmm27 or charmm36 force field and pre-equilibrated in NPT
>> >> >> conditions. I'll bevery thankfull to anybody who provide me with the
>> >> >> coordinates as well as itp file for such bilayer.
>> >> >>
>> >> >
>> >> > http://terpconnect.umd.edu/~jbklauda/research/download.html
>> >> >
>> >> > Google is your friend.  There are plenty more places to look.  A search 
>> >> > for
>> >> >
>> >> > "POPC CHARMM membrane coordinates" (without the quotes) does the trick.
>> >> >
>> >> > -Justin
>> >> >
>> >> > --
>> >> > 
>> >> >
>> >> > Justin A. Lemkul, Ph.D.
>> >> > Research Scientist
>> >> > 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
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>> >> >
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>> >
>> > --
>> >
>> > --
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>>

Re: [gmx-users] How to convert coarse-grained to fine-grained

Re: [gmx-users] Reduction of system dimensions

[gmx-users] Re: gmx-users Digest, Vol 104, Issue 94

Re: [gmx-users] Re: High density after NPT

Re: [gmx-users] How to convert coarse-grained to fine-grained

RE: [gmx-users] Energy Minimization/ NpT settling problem

[gmx-users] Energy Minimization/ NpT settling problem

[gmx-users] Re: High density after NPT

Re: [gmx-users] How to convert coarse-grained to fine-grained

Re: [gmx-users] using g_analyze for calculating distance autocorrelation functions

[gmx-users] using g_analyze for calculating distance autocorrelation functions

Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

[gmx-users] virtual sites with CHARMM lipids

Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

RE: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

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