[gmx-users] Re: cutoff for implicit solvent in gromacs4.5

[BIN ZHANG]

Dear Per:
Thanks for your reply.
I did start the simulation from an equilibrated structure. Instead of  
setting them to 0, if I simply use a large cut-off (say 1.6),  
everything works just fine.
Best,
Bin


============
Hi,

for implicit solvent, people generally use longer cut-offs, as you  
noted.

There can be many reasons for your seg. fault, however.
Did you do energy minimization before starting md?
Please also test the same system with using a cut-off to see if that  
works.

/Per



8 aug 2010 kl. 22.36 skrev BIN ZHANG:

> But the problem is with this set up, I will always get a  
"Segmentation fault" with gromacs VERSION 4.5-beta2.
>
> Is this supposed to be a bug or for this version, I can only use a  
large cutoff?

On Aug 8, 2010, at 10:56 PM, gmx-users-requ...@gromacs.org wrote:

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Today's Topics:

  1. Best forcefield for DMPC - Protein system (Deniz KARASU)
  2. Best forcefield for DMPC - Protein system (Deniz KARASU)
  3. cutoff for implicit solvent in gromacs4.5 (BIN ZHANG)
  4. Large output files and limited disk space. How do I        handle
     them? (NG HUI WEN)
  5. Re: Large output files and limited disk space. How do I
     handle them? (Mark Abraham)

From: Deniz KARASU <karasude...@gmail.com>
Date: August 8, 2010 8:45:08 AM PDT
To: gmx-users@gromacs.org
Subject: [gmx-users] Best forcefield for DMPC - Protein system
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>


Hi,

I am planing to use 53a6 ff for my membrane protein system. And I can
use Kukol 2009 lipid or Roger 2010 lipid and topology  so I wonder  
is there any
problem about 53a6 force field and what is the most suitable force
field for membrane protein systems?

I read from http://www.mail-archive.com/gmx-users@gromacs.org/msg27700.html
mail that there are some problems about 53a6 forcefield.


1) Kukol, A., 2009. Lipid models for united-atom molecular dynamics
simulations of proteins
2) D Poger, WF Van Gunsteren,  2010.  A new force field for simulating
phosphatidylcholine bilayers.

Thanks.
Deniz.




From: Deniz KARASU <karasude...@gmail.com>
Date: August 8, 2010 8:47:48 AM PDT
To: gmx-users@gromacs.org
Subject: [gmx-users] Best forcefield for DMPC - Protein system
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>


Hi,

I am planing to use 53a6 ff for my membrane protein system. And I can
use Kukol 2009 lipid or Roger 2010 lipid and topology  so I wonder  
is there any
problem about 53a6 force field and what is the most suitable force
field for membrane protein systems?

I read from http://www.mail-archive.com/gmx-users@gromacs.org/msg27700.html
mail that there are some problems about 53a6 forcefield.


1) Kukol, A., 2009. Lipid models for united-atom molecular dynamics
simulations of proteins
2) D Poger, WF Van Gunsteren,  2010.  A new force field for simulating
phosphatidylcholine bilayers.

Thanks.
Deniz.




From: BIN ZHANG <zhn...@gmail.com>
Date: August 8, 2010 1:36:39 PM PDT
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: [gmx-users] cutoff for implicit solvent in gromacs4.5
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>


Dear all:

I have a question about the appropriate cut-off usage in implicit  
solvent simulation. After googling for a while, I found most  
references mentioning using non cut-off for these type of  
simulations. For non cut-off,  I assume in gromacs using the  
following parameters:

coulombtype              = Cut-off
vdwtype                     = Cut-off
nstype                       = grid
nstlist                        = 0
rlist                            = 0
rcoulomb                  = 0
rvdw                         = 0

; implicit solvent options
implicit_solvent     =   GBSA
gb_epsilon_solvent   =   80
gb_algorithm         =   OBC
rgbradii                  = 0       ; need to be equal to rlist

But the problem is with this set up, I will always get a  
"Segmentation fault" with gromacs VERSION 4.5-beta2.

Is this supposed to be a bug or for this version, I can only use a  
large cutoff?

Thanks,
Bin





From: "NG HUI WEN" <huiwen...@nottingham.edu.my>
Date: August 8, 2010 8:04:57 PM PDT
To: <gmx-users@gromacs.org>
Subject: [gmx-users] Large output files and limited disk space. How  
do I handle them?
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>


Dear gmxusers,

I have a very basic question here which I hope someone could help me  
with. I was running a couple of simulations over the weekend on a  
shared cluster and both came to a stop for the same reasons:

Program mdrun_mpi, VERSION 4.0.7
Source code file: trnio.c, line: 252
File input/output error:
Cannot write trajectory frame; maybe you are out of quota?

Indeed there were quite a number of large files in my user directory  
(e.g. the .trr files and etc). I think the problems probably arise  
from the fact that (i) I am storing my trajectory as full  
precision .trr files and (ii) setting too small a value for nstxout  
and nstvout in .mdp.

I have seen some tutorials that suggested using "trjconv" to derive  
the reduced precision .xtc files from the .trr files and then  
discard the latter. My question is, would this be wise as I am not  
sure whether I would find myself needing these .trr files in the  
future.

Here's a snippet of my .mdp file. Am I saving my coordinates and  
velocities too frequently? If I were to increase this, are there any  
compelling factors that I need to take into considerations?
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 500000        ; 2 * 500000 = 1000 ps (1 ns)
dt              = 0.002         ; 2 fs
; 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

Many thanks for your help!

<<
Email has been scanned for viruses by UNMC email management service

>>



From: Mark Abraham <mark.abra...@anu.edu.au>
Date: August 8, 2010 10:55:50 PM PDT
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: Re: [gmx-users] Large output files and limited disk space.  
How do I handle them?
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>




----- Original Message -----
From: NG HUI WEN <huiwen...@nottingham.edu.my>
Date: Monday, August 9, 2010 13:17
Subject: [gmx-users] Large output files and limited disk space. How  
do I	handle them?
To: gmx-users@gromacs.org

> Dear gmxusers,
>
> I have a very basic question here which I hope someone could help  
me with. I was running a couple of simulations over the weekend on a  
shared cluster and both came to a stop for the same reasons:
>
> Program mdrun_mpi, VERSION 4.0.7
> Source code file: trnio.c, line: 252
> File input/output error:
> Cannot write trajectory frame; maybe you are out of quota?
>
> Indeed there were quite a number of large files in my user  
directory (e.g. the .trr files and etc). I think the problems  
probably arise from the fact that (i) I am storing my trajectory as  
full precision .trr files and (ii) setting too small a value for  
nstxout and nstvout in .mdp.
>
> I have seen some tutorials that suggested using "trjconv" to  
derive the reduced precision .xtc files from the .trr files and then  
discard the latter. My question is, would this be wise as I am not  
sure whether I would find myself needing these .trr files in the  
future.
>
> Here's a snippet of my .mdp file. Am I saving my coordinates and  
velocities too frequently? If I were to increase this, are there any  
compelling factors that I need to take into considerations?
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 500000        ; 2 * 500000 = 1000 ps (1 ns)
> dt              = 0.002         ; 2 fs
> ; 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

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

Unless you know you need full precision data for some expected  
analyses, I'd expect most people want nstxout/nstvout every few  
nanoseconds to enable restarts (possible, but unlikely to be  
needed). For most analyses, using nstxtcout with suitable output  
groups is at least an order of magnitude more space-efficient. Also  
consider how large nstenergy should be.

Mark



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