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

BIN ZHANG zhngbn at gmail.com
Mon Aug 9 18:43:23 CEST 2010


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-request at gromacs.org wrote:

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> Today's Topics:
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>   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 <karasudeniz at gmail.com>
> Date: August 8, 2010 8:45:08 AM PDT
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Best forcefield for DMPC - Protein system
> Reply-To: Discussion list for GROMACS users <gmx-users at 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 <karasudeniz at gmail.com>
> Date: August 8, 2010 8:47:48 AM PDT
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Best forcefield for DMPC - Protein system
> Reply-To: Discussion list for GROMACS users <gmx-users at 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 <zhngbn at gmail.com>
> Date: August 8, 2010 1:36:39 PM PDT
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: [gmx-users] cutoff for implicit solvent in gromacs4.5
> Reply-To: Discussion list for GROMACS users <gmx-users at 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.Ng at nottingham.edu.my>
> Date: August 8, 2010 8:04:57 PM PDT
> To: <gmx-users at 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 at 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.abraham at anu.edu.au>
> Date: August 8, 2010 10:55:50 PM PDT
> To: Discussion list for GROMACS users <gmx-users at 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 at gromacs.org>
>
>
>
>
> ----- Original Message -----
> From: NG HUI WEN <HuiWen.Ng at 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 at 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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