AW: AW: AW: AW: [gmx-users] g_current

2013-02-26 Thread Florian Dommert
Hi, I am using the release branch of 4.5. /Flo --- Florian Dommert Dipl. Phys. Institut für Computerphysik Universität Stuttgart Allmandring 3 D-70569 Stuttgart Tel.: 0711-68563613 Fax: 0711-68563658 > -Ursprüngliche Nachricht- > Von: gmx-users-boun...@gromacs.org [mailto:gmx-user

[gmx-users] lennard jones 6-12 value setting

2013-02-26 Thread 라지브간디
Dear gmx, I want set the particular value of lennard jones 6-12 for NO ligand for my simulation. I believe it has be mentioned in topology file created by force field. My questions is how to set these value in topology which created by CHARMM 27 ff? Thanks in advance. -- gmx-users mailing l

Re: [gmx-users] Re: Gromacs 4.6 Installation under Cygwin

2013-02-26 Thread Mirco Wahab
Hi Mike On 25.02.2013 17:25, toma0...@umn.edu wrote: ... Estimated maximum distance required for P-LINCS: 0.810 nm ... Domain decomposition grid 4 x 2 x 1, separate PME nodes 0 Do your runs use PME and/or P-LINCS? Maybe you could point out the problem by disabling each or both in yout .mdp fi

Re: [gmx-users] gbsa.itp for amber ff

2013-02-26 Thread Justin Lemkul
On 2/25/13 10:05 PM, Yun Shi wrote: Hi all, If I want do MD simulation with amber ff and implicit solvent, would including gbsa.itp in .top file and specifying parameters in .mdp as follows be sufficient? implicit_solvent = GBSA gb_algorithm = OBC nstgbradii = 1.0 rgbradii =

Re: [gmx-users] Error during npt equilibration in coarse grained simulation

2013-02-26 Thread Justin Lemkul
On 2/26/13 12:51 AM, Anu Chandran wrote: Sir, I have tried Berendsen barostat for Pcoupl. Still I get the same error. So have a look at the other recommendations on the page I linked. Thermostat instability is just one possibility. We have had numerous reports, just in the last week, o

Re: [gmx-users] Why not PBC for implicit solvent?

2013-02-26 Thread Justin Lemkul
On 2/25/13 10:30 PM, Yun Shi wrote: Hi everyone, Previous posts mentioned setting pbc = none for MD simulations with implicit solvent. But I am trying to see the behavior of certain concentration of ligands (small molecules, no big biomolecules) in solvent, so I wonder if setting pbc = xyz wou

Re: [gmx-users] lennard jones 6-12 value setting

2013-02-26 Thread Justin Lemkul
On 2/26/13 4:33 AM, 라지브간디 wrote: Dear gmx, I want set the particular value of lennard jones 6-12 for NO ligand for my simulation. I believe it has be mentioned in topology file created by force field. My questions is how to set these value in topology which created by CHARMM 27 ff? The d

[gmx-users] help

2013-02-26 Thread Sjøli Stian
dear gmx-users, this is a stupid question (and partially a test of use). I cant find any information on how to use/modify maxvarn as a parameter for grompp. Can you point to examples or literature? sincerely user -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailma

Re: [gmx-users] help

2013-02-26 Thread Justin Lemkul
On 2/26/13 7:46 AM, Sjøli Stian wrote: dear gmx-users, this is a stupid question (and partially a test of use). I cant find any information on how to use/modify maxvarn as a parameter for grompp. Can you point to examples or literature? Consider the help text: -maxwarn int0

Re: [gmx-users] request

2013-02-26 Thread Justin Lemkul
Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. I am CC'ing the list and ask that further comments and questions be posted there. On 2/26/13 8:40 AM, Group Gro wrote: Dear Prof. Justin, Thanks a lot about your recommendation. We couldn't sol

RE: [gmx-users] Why not PBC for implicit solvent?

2013-02-26 Thread Sebastien Cote
Dear Justin (and Yun), Since our last discussion on implicit solvent simulations, I have read a bit more about how cutoffs in GBSA (or variants) implicit solvent simulations are used in other softwares such as AMBER, CHARMM and NAMD. It appears to me that many use switch or shift cutoffs. Have

[gmx-users] Re: genion

2013-02-26 Thread Justin Lemkul
For the fourth time in two days, I'll start with: Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. I am CC'ing the list and ask that further comments and questions be posted there. On 2/26/13 9:03 AM, Samadashvili Nino wrote: Dear Justin,

Re: [gmx-users] Why not PBC for implicit solvent?

2013-02-26 Thread Justin Lemkul
On 2/26/13 9:23 AM, Sebastien Cote wrote: Dear Justin (and Yun), Since our last discussion on implicit solvent simulations, I have read a bit more about how cutoffs in GBSA (or variants) implicit solvent simulations are used in other softwares such as AMBER, CHARMM and NAMD. It appears to me

[gmx-users] How to differenciate Decane and Dodecane with the Martini force field

2013-02-26 Thread ABEL Stephane 175950
Hello all, Sorry if it is not the right place to ask the question, but i have a doubt about the topology for alkanes with MARTINI Since in Martini - the default mapping is 4 AA -> 1 bead - that in the martini_"v2.0_solvents.itp file" it is stated that the DECANE has the same topology as dode

Re: [gmx-users] How to differenciate Decane and Dodecane with the Martini force field

2013-02-26 Thread Tsjerk Wassenaar
Hi Stephane, It's one of the caveats of a reduced resolution model. You loose detail, like the distinction between decane and dodecane. Although, there are two bonds and an angle to make a difference. > Additionally, can i change of the mass of each bead the mass of Decane/3 in > the itp file in

[gmx-users] About intial DPPC Pdb

2013-02-26 Thread vidhya sankar
Dear  justin Thank you for your Previous Reply   I am Doing Lipid Protein Simulation .  As stated in your Website for Protein Lipid Tutorial  I  have Downloaded DPPC.pdb . and Did simulation As per Procedure ?  My Question is  Instead of Taking DPPC.pdb   Can i take Following  Pdb  for Embedd

Re: [gmx-users] About intial DPPC Pdb

2013-02-26 Thread Justin Lemkul
On 2/26/13 11:01 AM, vidhya sankar wrote: Dear justin Thank you for your Previous Reply I am Doing Lipid Protein Simulation . As stated in your Website for Protein Lipid Tutorial I have Downloaded DPPC.pdb . and Did simulation As per Procedure ? My Question is Instead of Taking DP

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread Justin Lemkul
On 2/26/13 11:30 AM, francesco oteri wrote: Dear gromacs users, in Bjelkmar et al. (2010) where the implementation of CHARMM in GROMACS is described, the authors say that: "Electrostatics was treated with particle-mesh Ewald (PME), using a short-range cutoff of 1.2 nm, and van der Waals intera

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread francesco oteri
Thank you Justin, I added rlistlong = 1.4 but still grompp complains: NOTE 1 [file 02md.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. Why doesn't grompp looks for rlistlong value? Francesco 2013/2/26 Justin Lemkul > > >

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread Justin Lemkul
On 2/26/13 11:47 AM, francesco oteri wrote: Thank you Justin, I added rlistlong = 1.4 but still grompp complains: NOTE 1 [file 02md.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. Why doesn't grompp looks for rlistlong va

Re: AW: AW: AW: AW: [gmx-users] g_current

2013-02-26 Thread Nilesh Dhumal
Hello, I didn't get any segmental fault if I use Gromacs Version 4.5.5. g_current -f md.trr -s md.tpr -mc Program didn't write the mc.xvg Average translational dipole moment is zero. Average translational dipole moment M_J [enm] after 15001 frames (|M|^2): -0.00 -0.00 -0.00 (0.000

[gmx-users] mdrun WARING and crash

2013-02-26 Thread L.Liu
Dear all, I got WARNING after mdrun, which says: "WARNING: Listed nonbonded interaction between particles 794 and 797 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread francesco oteri
I am using 4.5.5...Is it OK? 2013/2/26 Justin Lemkul > > > On 2/26/13 11:47 AM, francesco oteri wrote: > >> Thank you Justin, >> I added >> rlistlong = 1.4 >> >> but still grompp complains: >> NOTE 1 [file 02md.mdp]: >>For energy conservation with switch/shift potentials, rlist should

Re: [gmx-users] mdrun WARING and crash

2013-02-26 Thread Justin Lemkul
On 2/26/13 11:57 AM, l@utwente.nl wrote: Dear all, I got WARNING after mdrun, which says: "WARNING: Listed nonbonded interaction between particles 794 and 797 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction insid

Re: [gmx-users] g_bar for larger systems (protein-protein interaction)

2013-02-26 Thread Ricardo Soares
On Mon, 25 Feb 2013 15:55:05 -0500, Michael Shirts wrote > My personal opinion is that for large protein-protein calculations, > the free energy should be computed through potential of mean force > calculations, NOT alchemical methods, using the endpoints (properly > corrected) to determine the fre

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread Justin Lemkul
On 2/26/13 12:01 PM, francesco oteri wrote: I am using 4.5.5...Is it OK? If it's giving a note about that, then clearly not. Try 4.6. But as I said, there's nothing actually wrong. -Justin 2013/2/26 Justin Lemkul On 2/26/13 11:47 AM, francesco oteri wrote: Thank you Justin, I

[gmx-users] Re: [gmx-developers] 【file tpx versio】how to convert the version

2013-02-26 Thread Justin Lemkul
Please post usage questions to gmx-users, not gmx-developers. I will CC this reply to gmx-users and ask that the discussion continue there. On 2/26/13 12:05 PM, 何斌 wrote: Hi: everyone. I has got that the error: //

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread francesco oteri
Thank you so much for the help! 2013/2/26 Justin Lemkul > > > On 2/26/13 12:01 PM, francesco oteri wrote: > >> I am using 4.5.5...Is it OK? >> >> > If it's giving a note about that, then clearly not. Try 4.6. But as I > said, there's nothing actually wrong. > > -Justin > > >> 2013/2/26 Justin

[gmx-users] Re: How to differenciate Decane and Dodecane with the Martini force field

2013-02-26 Thread ABEL Stephane 175950
Thank you Tsjerk for your quick response. A bientot Stephane -- Message: 2 Date: Tue, 26 Feb 2013 16:53:51 +0100 From: Tsjerk Wassenaar Subject: Re: [gmx-users] How to differenciate Decane and Dodecane with the Martini force field To: Discussion list f

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread francesco oteri
I downloaded and installed gromacs-4.6 but I get the warning WARNING 1 [file NVE.mdp]: The sum of the two largest charge group radii (0.067845) is larger than rlist (1.20) - rvdw (1.20) I attacch the files you may need to solve the problem NVE.mdp

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread Justin Lemkul
On 2/26/13 2:06 PM, francesco oteri wrote: I downloaded and installed gromacs-4.6 but I get the warning WARNING 1 [file NVE.mdp]: The sum of the two largest charge group radii (0.067845) is larger than rlist (1.20) - rvdw (1.20) I attacch the files you may need to solve the prob

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread Mark Abraham
That looks like (at least) a grompp bug leading to the error. Can you attach a .tpr file to http://redmine.gromacs.org/issues/1164 please Francesco? Mark On Tue, Feb 26, 2013 at 8:09 PM, Justin Lemkul wrote: > > > On 2/26/13 2:06 PM, francesco oteri wrote: > >> I downloaded and installed gromac

Re: [gmx-users] The sum of the two largest charge group radii is larger than rlist - rvdw (because rlist < rvdw)

2013-02-26 Thread Mark Abraham
On Tue, Feb 26, 2013 at 8:56 PM, Christopher Neale < chris.ne...@mail.utoronto.ca> wrote: > Dear users: > > I am experimenting with the "Stockholm" lipid parameters (Slipids). I > downloaded the recommended .mdp file from the developers of this force > field ( http://people.su.se/~jjm/Stockholm_Li

Re: [gmx-users] Coupling only a variable solvent subgroup to the thermostat

2013-02-26 Thread Mark Abraham
Only your kind of scripting approach will be able to do this. While we do plan to provide this kind of "dynamic selection" for the analysis tools in 5.0, I'd be surprised if we found time/need to do it for mdrun. Whether it's a useful thing to do, I have no real idea. Mark On Mon, Feb 25, 2013 a

Re: [gmx-users] Re: Gromacs 4.6 Installation under Cygwin

2013-02-26 Thread toma0052
Hello, It looks like the problem might be in my mdp settings. I am using the MARTINI force field which uses shift functions for both electrostatics and vdw which are only available in the group-based cut-off scheme. OpenMP doesn't seem to run with the group-based cut-off scheme, just Verlet

Re: [gmx-users] Re: Gromacs 4.6 Installation under Cygwin

2013-02-26 Thread Szilárd Páll
Hi, That is a likely cause. I can not comment with full certainty on the use of MARTINI with the Verlet scheme & without shifts, but I know that it is a topic that's being investigated and hopefully other can comment on it. However, the hanging should definitely not happen, but instead an error s

Re: [gmx-users] Re: Gromacs 4.6 Installation under Cygwin

2013-02-26 Thread Szilárd Páll
I've a few more comments. First of all, please upload to redmine the full mdrun.debug output! It looks like the detection of the number of cores in your machine does not work with cygwin because when you only set "-ntmp 1" N OpenMP threads should be auto-set (N=#cores), but based on your output it

Re: [gmx-users] Number of atoms is very high

2013-02-26 Thread Justin Lemkul
On 2/26/13 5:50 PM, Divya Sunil wrote: Hello I have a protein consists of 2303 atoms. I simulated it in water using cubic box. As the protein has a long tail, the no. of water molecules to fill the box is very high (132235). After simulation I converted the .gro file to .pdb and in which I hav

Re: [gmx-users] Number of atoms is very high

2013-02-26 Thread Divya Sunil
ok..thank you very much On 26 February 2013 23:54, Justin Lemkul wrote: > > > On 2/26/13 5:50 PM, Divya Sunil wrote: > >> Hello >> >> I have a protein consists of 2303 atoms. I simulated it in water using >> cubic box. As the protein has a long tail, the no. of water molecules to >> fill the box

Re: [gmx-users] Number of atoms is very high

2013-02-26 Thread Justin Lemkul
On 2/26/13 6:37 PM, Divya Sunil wrote: ok..thank you very much The other thing I forgot to mention is that perhaps you can use a different box shape. Dodecahedral and octahedral require a lot fewer water molecules than a cubic box of equivalent periodic distance. -Justin On 26 Februar

[gmx-users] Problem with OpenMP+MPI

2013-02-26 Thread jesmin jahan
Dear Gromacs Users, I am trying to run the following command on gromacs 4.6 mdrun -ntmpi 2 -ntomp 6 -s imd.tpr But I am getting the following error OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet Does any one know a solution

[gmx-users] Re: The sum of the two largest charge group radii is larger than rlist - rvdw (because rlist < rvdw)

2013-02-26 Thread Joakim Jämbeck
Dear Chris, We have used the following settings in our recent work (http://pubs.rsc.org/en/content/articlelanding/2013/CP/C3CP44472D): coulombtype=pme rcoulomb=1.0 rlist=1.0 vdw-type=cut-off rvdw=1.4 dispcorr=enerpres And this works fine without any notes etc from grompp, and you do not have to