[gmx-users] Re: gmx-users Digest, Vol 96, Issue 189
PAVAN PAYGHAN
pavanapex at gmail.com
Thu Apr 26 14:47:49 CEST 2012
Dear Mark,
Thanks a lot for the reply and highlighting the cause of error that I was
facing.
Still can it be possible to overcome the same error with the available
facility.
Pavan Payghan
On Thu, Apr 26, 2012 at 9:55 AM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Free Energy calcualtions (Sai Kumar Ramadugu)
> 2. How to choose two atoms at the same time, using g_select
> selection.dat (mu xiaojia)
> 3. Re: How to choose two atoms at the same time, using g_select
> selection.dat (Justin A. Lemkul)
> 4. Re: why it is so slow in Blue gene? (Mark Abraham)
> 5. Fwd: Error: coordinate file does not match with the topology
> file (Mark Abraham)
> 6. Re: How to increase the ratio of cell size to constrain
> length per error message (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 25 Apr 2012 16:05:05 -0500
> From: Sai Kumar Ramadugu <sramadugu at gmail.com>
> Subject: [gmx-users] Free Energy calcualtions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CAO6uzQUPcXNcot6qbkWLrrrifpk2Y3ciCfFTs7+FwYyJrb0smg at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Gromacs Users,
> I want to mutate a glutamate in my protein to alanine in presence of a
> ligand.
> With glutamate, the protein charge is -3. To neutralize the system, I added
> 3K+ ions.
> Now when I mutate GLU to ALA, the charge in state_B will be +1 (protein -2
> + 3K+).
>
> Right now I'm in the charge part of the mutation. Once this is successful,
> I will include the VDW mutation too.
>
> I have added the mutation details of Glu to Ala residue in the topology in
> [atoms], [bonds], [angles] and [dihedrals] sections.
>
> After I run the grompp command, the result says that my State_B topology
> has +1 charge since I am not including mutation of one K+ ion to neutral K+
> ion.
> How can I mutate 1 particular K+ to K atom and subsequently to a dummy
> atom? Since I'm using OPLS force field, we have ions.itp to be used in the
> topology file, changing one K+ is making it troublesome for me to implement
> in the topology file.
> Any suggestions are helpful.
>
> Thanks for your time.
>
> Regards
> Sai
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> ------------------------------
>
> Message: 2
> Date: Wed, 25 Apr 2012 20:19:22 -0500
> From: mu xiaojia <muxiaojia2010 at gmail.com>
> Subject: [gmx-users] How to choose two atoms at the same time, using
> g_select selection.dat
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CABSFTFqreE885zmhdQq6n2qrjcKo2c-SdupOT_utJbXKKyoqLw at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear gmx users,
>
> I may have a silly question, how to make a group of two atoms from the same
> molecule?
>
> e.g, I want to make an "HN" group of both H and N from my 2nd residue,
>
> I know for single one, commands in *.dat file is like:
>
> nameN = resnr 2 and name N;
> nameH = resnr 2 and name H;
>
> nameN;
> nameH;
>
> I guess "merge" or "plus" might be helpful,I think it should be done
> something like: "nameN_H = resnr 2 and name N ?? resnr 2 and name H", so it
> is an intramolecular combination between N and H; it shouldn't be done
> afterwards, otherwise it would be an intermolecular combination.
>
> Thanks very much! g_select is really powerful, and hopefully there would be
> more examples.
>
> Jia
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> ------------------------------
>
> Message: 3
> Date: Wed, 25 Apr 2012 21:24:21 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] How to choose two atoms at the same time,
> using g_select selection.dat
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F98A3C5.8040904 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 4/25/12 9:19 PM, mu xiaojia wrote:
> > Dear gmx users,
> >
> > I may have a silly question, how to make a group of two atoms from the
> same
> > molecule?
> >
> > e.g, I want to make an "HN" group of both H and N from my 2nd residue,
> >
> > I know for single one, commands in *.dat file is like:
> >
> > nameN = resnr 2 and name N;
> > nameH = resnr 2 and name H;
> >
> > nameN;
> > nameH;
> >
> > I guess "merge" or "plus" might be helpful,I think it should be done
> something
> > like: "nameN_H = resnr 2 and name N ?? resnr 2 and name H", so it is an
> > intramolecular combination between N and H; it shouldn't be done
> afterwards,
> > otherwise it would be an intermolecular combination.
> >
> > Thanks very much! g_select is really powerful, and hopefully there would
> be more
> > examples.
> >
>
> g_select is more suited for complex groups that are dynamic or otherwise
> based
> on geometric criteria. If you're trying to make a simple group that
> consists of
> 2 atoms, make_ndx is easier, and using a plain text editor will be
> easiest, i.e.:
>
> [ my_group ]
> 1 2
>
> -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
>
> ========================================
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 26 Apr 2012 14:04:49 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] why it is so slow in Blue gene?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F98C961.9030105 at anu.edu.au>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> On 25/04/2012 3:24 PM, Albert wrote:
> > hello:
> >
> > it is blue gene P. And the gromacs is single precision in the
> > cluster. Getting Loaded...And the administrator told me that I have to
> > use the multiples of 32 in the bg_size parameter. The number specified
> > in "-np" should be 4 times bg_size.
>
> Yes, but your system is too small to make use of 128 processors. Also,
> get rid of -launch and -nt from your command line, since they do nothing.
>
> > It is even slower than my own workstation with 16 core.........
> >
> >
> >
> >
> > here is the log file I get:
>
> No, that's the stdout file. Look at the end of the .log file.
>
> >
> > -------------log----------------
> > Reading file npt_01.tpr, VERSION 4.5.5 (single precision)
> > Loaded with Money
> >
> > Will use 112 particle-particle and 16 PME only nodes
>
> This is guaranteed to lead to woeful performance with your .mdp
> settings, but you will have to look towards the beginning of the .log
> file to find out why mdrun selected this. Odds are good that your system
> size is so small that the minimum particle-particle cell size
> (constrained by rcoulomb) doesn't give mdrun any good options that use
> all the processors. You'd likely get better raw performance with twice
> the number of atoms or half the number of processors.
>
> Mark
>
> > This is a guess, check the performance at the end of the log file
> > Making 3D domain decomposition 4 x 4 x 7
> > starting mdrun 'GRowing Old MAkes el Chrono Sweat'
> > 500000 steps, 500.0 ps.
> > step 0
> > vol 0.64! imb F 16% pme/F 0.22 step 100, will finish Wed Apr 25
> > 18:28:06 2012
> > vol 0.65! imb F 17% pme/F 0.21 step 200, will finish Wed Apr 25
> > 18:09:54 2012
> > vol 0.67! imb F 18% pme/F 0.21 step 300, will finish Wed Apr 25
> > 18:03:12 2012
> > vol 0.69! imb F 18% pme/F 0.21 step 400, will finish Wed Apr 25
> > 17:58:25 2012
> > vol 0.67! imb F 19% pme/F 0.21 step 500, will finish Wed Apr 25
> > 17:55:26 2012
> > vol 0.68! imb F 19% pme/F 0.22 step 600, will finish Wed Apr 25
> > 17:53:31 2012
> > vol 0.68! imb F 19% pme/F 0.22 step 700, will finish Wed Apr 25
> > 17:51:57 2012
> > vol 0.68! imb F 19% pme/F 0.22 step 800, will finish Wed Apr 25
> > 17:50:32 2012
> > vol 0.68! imb F 20% pme/F 0.22 step 900, will finish Wed Apr 25
> > 17:49:14 2012
> > vol 0.67! imb F 21% pme/F 0.22 step 1000, will finish Wed Apr 25
> > 17:48:13 2012
> > vol 0.68! imb F 20% pme/F 0.22 step 1100, will finish Wed Apr 25
> > 17:47:28 2012
> > vol 0.67! imb F 21% pme/F 0.22 step 1200, will finish Wed Apr 25
> > 17:46:50 2012
> > vol 0.67! imb F 21% pme/F 0.22 step 1300, will finish Wed Apr 25
> > 17:46:15 2012
> >
> >
> >
> > On 04/24/2012 06:01 PM, Hannes Loeffler wrote:
> >> On Tue, 24 Apr 2012 15:42:15 +0200
> >> Albert<mailmd2011 at gmail.com> wrote:
> >>
> >>> hello:
> >>>
> >>> I am running a 60,000 atom system with 128 core in a blue gene
> >>> cluster. and it is only 1ns/day.... here is the script I used for
> >> You don't give any information what exact system that is (L/P/Q?), if
> >> you run single or double precision and what force field you are using.
> >> But for a similar sized system using a united atom force field in
> >> single precision we find about 4 ns/day on a BlueGene/P (see our
> >> benchmarking reports on
> >> http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx). I would
> >> expect a run with the CHARMM 27 force field in double precision to be
> >> roughly 3 times slower. We found scaling to 128 cores to be
> >> reasonably good. Also, check our report for problems when compiling
> >> with higher optimisation.
> >>
> >> Hannes.
> >
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 26 Apr 2012 14:13:06 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: [gmx-users] Fwd: Error: coordinate file does not match with
> the topology file
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F98CB52.1060606 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Please do not make unsolicited general GROMACS inquiries to private
> email addresses. The mailing lists exist for these kinds of purposes.
>
> On point, you cannot be helped unless you provide the command lines that
> you used and describe the objectives you were trying to achieve.
> Whatever changes you make to one of the coordinate and .top file must be
> matched in the other.
>
> Mark
>
> -------- Original Message --------
> Subject: Error: coordinate file does not match with the topology
> file
> Date: Wed, 25 Apr 2012 02:05:45 +0800 (SGT)
> From: sonali shinde <shindesonali14 at yahoo.co.in>
> Reply-To: sonali shinde <shindesonali14 at yahoo.co.in>
> To: Mark.Abraham at anu.edu.au <mark.abraham at anu.edu.au>
>
>
>
>
> ----- Forwarded Message -----
> *From:* sonali shinde <shindesonali14 at yahoo.co.in>
> *To:* vini k <vineetha_mandlik at yahoo.co.in>
> *Sent:* Monday, 23 April 2012 6:48 PM
> *Subject:* Error: coordinate file does not match with the topology file
>
> Dear Sir,
> I am a user of gromacs 4.0 for molecular dynamic study of
> a protein molecule. I have generated trajectory file before using the
> same commands that I use now. Recently I am suffering some problem using
> Gromacs , my coordinate file does not matches with the topology file.I
> have attached the pdb file protein, .gro and .top file . I have
> encountered same error a number of times with three different
> proteins.Please suggest the answer for the same.
> Thanking you.
>
>
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> ------------------------------
>
> Message: 6
> Date: Thu, 26 Apr 2012 14:24:53 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] How to increase the ratio of cell size to
> constrain length per error message
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F98CE15.4040309 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 25/04/2012 6:28 AM, PAVAN PAYGHAN wrote:
> >
> > Dear Gromacs Users,
> >
> > I am using gromacs version is 4.5.3.and running my jobs on single node
> > with 8 cores.
> >
> > I have two different systems which contain about 425000 atoms (protein
> > + Lipid +SOL) one with bound ligand
> >
> > and another one unbound protein.I have successfully reached up to
> > NPT equilibration run step,
> >
>
> It is a poor idea to do equilibration with Parinello-Rahman, which is
> unstable when the system is not already close to equilibrium. For some
> reason people still do it, despite at least a post per week on this list
> suggesting against it, and a warning in the manual. Use Berendsen to fix
> the density, then equilibrate further with P-R to get the right ensemble.
>
> > now I want to continue the same for production run. Without ligand I
> > am able to run successfully But the same system with ligand is
> > crashing with following error-
> >
> > D D cell 1 0 0 could only obtain 1520 of the 1521 atoms that are
> >
> > are connected via constraints from the neighbouring cells
> >
> > This probably means your constraint length are too long
> >
> > compared to the domain decomposition cell size.
> >
> > Decrease the number of domain decomposition grid cells or lincs_order.
> >
>
> I'd rather expect your system was blowing up because of the above issue.
> Perhaps the suggestion in the error message is not as complete as could
> be desired - you have so many atoms per processor that the constraint
> length would normally be tiny with respect to the cell size. So I think
> the things you have tried below are rearranging the deck chairs on the
> Titanic.
>
> Mark
>
> > Accordingly following the suggestions given in the error I tried to
> > solve it with
> >
> > Following log file and changed,
> >
> > 1.1. -rcon
> >
> > Estimated maximum distance required for p-lincs was 0.877 thus
> > I increased it to 0.900
> >
> > then it thrown another error.
> >
> > The initial cell size (0.877) is smaller than the cell size limit
> > (0.900)
> >
> >
> > 2 .Then I tried to increase the --dds and --rdd from original values
> > of 1.25 and 0.623 to 1.30 and 0.670 respectively.
> >
> > But it does not help and ended with run crash.
> >
> > /*What I did was logical or I did it wrongly?*/
> >
> > /*Now can anyone please suggest me the appropriate way to deal with
> > the problem mentioned above? */
> >
> > As I want the continuation of the same run without altering the output
> > after change in the parameters (As I have to compare the output with
> > unbound protein run thus can't afford change in output with change in
> > parameters)
> >
> > I know that I need to change some of the parameters in .mdp file such as
> >
> > fourierspacing from 0.16 to 0.12 and on the contrary increase the
> > pme_order from say 4 to 6.
> >
> > /*But as asked above by doing so the output will not or will be the
> > exact continuation run?*/
> >
> > /*How to increase the ratio of cell size to constrain length per error
> > message?*/
> >
> > /*If any better way of doing so without changing the output please
> > suggest,*/
> >
> > I am suffering from the same problem since long,
> >
> > Please help me .Please see the mdp file for the reference.
> >
> > integrator = md
> >
> > nsteps = 10000000
> >
> > dt = 0.002 ; 2 fs
> > > >
> > ; Output control
> > nstxout = 1000 ;
> > nstvout = 1000 ;
> > nstxtcout = 1000 ;
> >
> > nstenergy = 1000 ;
> >
> > nstlog = 1000 ;
> > ; Bond parameters
> > continuation = yes ; Restarting after NPT
> > constraint_algorithm = lincs ; holonomic constraints
> > constraints = all-bonds ; all bonds (even heavy atom-H
> > bonds)
> > lincs_iter = 1 ; accuracy of LINCS
> > lincs_order = 4
> >
> > ; Neighborsearching
> > ns_type = grid
> > nstlist = 5
> >
> > rlist = 1.2
> > rcoulomb = 1.2
> > rvdw = 1.2
> > ; Electrostatics
> > coulombtype = PME
> > pme_order = 4
> > fourierspacing = 0.16
> > tcoupl = Nose-Hoover
> > tc-grps = Protein P SOL_NA_CL ;
> > tau_t = 0.5 0.5 0.5
> > ref_t = 323 323 323 group, in K
> > ; Pressure coupling is on
> > pcoupl = Parrinello-Rahman ;
> >
> > pcoupltype = semiisotropic
> > tau_p = 2.0 ; time
> > ref_p = 1.0 1.0 ; reference
> > compressibility = 4.5e-5 4.5e-5 ;
> >
> > ; Periodic boundary conditions
> > pbc = xyz ; 3-D PBC
> >
> > ; Dispersion correction
> > DispCorr = EnerPres ; account for cut-off vdW scheme
> >
> > ; Velocity generation
> > gen_vel = no
> >
> > Thanking in Advance
> >
> >
> >
>
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> End of gmx-users Digest, Vol 96, Issue 189
> ******************************************
>
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