[gmx-users] About rotational restraint

Hi! I'm applying COM pull on a two-domain protein by fixing the distance between the centers of mass of each domain with an umbrella potential. However, I find that the domains can rotate so that the inner surfaces of each domain are not parallel any more. How can I apply a rotational restraint so

Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

2009/8/10 Mark Abraham > Lee Soin wrote: > >> Hello! >> Sorry to bother you again, but I have another question. I have written a >> topology file of two water molecules to test the pair interaction. Here is >> part of my topology file: >> >> [ m

Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

. 2009/7/28 Mark Abraham > Lee Soin wrote: > >> So there is no place to specify electrostatic interactions for pair >> interactions? >> > > No. The charges are specified in the [ atoms ] directive. Read the example > in chapter 5. > > > Mark >

[gmx-users] What are the random factors in mdrun?

Hello! I am confused about random factors in GROMACS, because I find that different runs of the same .tpr file do not generate identical results. I know that Langevin dynamics introduces random forces, but what are the other random factors in GROMACS? Many thanks in advance. -- SUN Li Department

Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

So there is no place to specify electrostatic interactions for pair interactions? 2009/7/27 Mark Abraham > Lee Soin wrote: > >> I see in the .top file generated by pdb2gmx: >> [ pairs ] >> ; aiaj functc0c1c2c3 >&

Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

? Thanks! 2009/7/27 Mark Abraham > Lee Soin wrote: > >> My problem is actually as follows: >> > > Please describe in as full detail as reasonable the first time :-) > > I have three groups of atoms: A, B and C. Now I want to keep full >> interaction betw

Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

s are specified for each atom, so is there any way to treat the interaction pairwise? 2009/7/26 Mark Abraham > Lee Soin wrote: > >> Hello! >> I've read from the manual that the mdp option energygrp_excl can exclude >> pairs of energy groups for non-bonded intera

[gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

Hello! I've read from the manual that the mdp option energygrp_excl can exclude pairs of energy groups for non-bonded interactions. But now I would like to remove all other non-bonded interactions but retain the repulsive part of the VDW interaction for a pair of energy group. Is there a way to do

Re: [gmx-users] Probably a bug in nstenergy?

userreal1= 0 userreal2= 0 userreal3= 0 userreal4= 0 2009/4/20 Mark Abraham > Lee Soin wrote: > >> Hello! >> I'm experiencing a strange thing. I've tried to set nstenergy in .mdp file >> to various va

[gmx-users] Probably a bug in nstenergy?

Hello! I'm experiencing a strange thing. I've tried to set nstenergy in .mdp file to various values(0, 1, 100) but there seems to be no change in the output frequency in energy file and the file always attains several gigabytes easily. Probably a bug? -- SUN Li Department of Physics Nanjing U

Re: [gmx-users] LINCS warnings generated in NPT ensemble and not in NVT

The difference between "restraints" and "constraints" is indeed something I'm aware of :-) Even though distance restraint between COM of two domains worked just OK for me, I would prefer to use distance constraint since that will introduce fewer artifacts and can fix the distance between two domain

[gmx-users] LINCS warnings generated in NPT ensemble and not in NVT

Hello! I'm using COM pulling with distance constraint between two domains of a protein. The energy minimization and a 100-ps equilibrating process in the NPT ensemble with position restraints on protein atoms all passed OK. Then I applied a distance constraint between COM of two domains and perform

[gmx-users] Questions about urea.itp

Hello! Can the GROMACS topology file urea.itp be used with the OPLS force field? In urea.itp there are two sets of parameters, separated by "#ifdef" directives. Which set should be used? Thanks! -- SUN Li Department of Physics Nanjing University, China

[gmx-users] About pull force in COM pulling

Hello! I'm using COM pulling in GROMACS. Something I'm not clear about: (1) Is the pull force in the output file pullf.xvg just the spring force in umbrella pulling and the constraint force in constraint pulling? (2) In .mdp file, "pull_geometry" is specified as "distance". Then, what is the positi

[gmx-users] maintaining the overall conformation of a protein during simulation

Hello! I want to maintain the overall conformation of a protein during simulation. Is it recommended that I (1) use distance restraint generated by genrestr -disre (2) use distance constraint generated by genrestr -constr or (3) specify in [ bonds ] type 6 for each pair of C-alpha atoms Thanks! -

[gmx-users] Can make_ndx generate indices only for heavy atoms?

Hello, all! Can make_ndx generate indices only for heavy atoms or C-alpha atoms in a specified range of residues? And how? Thanks! -- SUN Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org http://www.g

Re: [gmx-users] How to handle incomplete PDB file?

Then what should I do? 2009/3/3 Justin A. Lemkul > > > Justin A. Lemkul wrote: > > Specifying -missing in pdb2gmx doesn't work. >>> >> > Also, don't do this. Note from the pdb2gmx documentation that this is > "dangerous." You will end up with incomplete amino acids, fractional > charges, and

[gmx-users] How to handle incomplete PDB file?

Hello! While processing a PDB file, pdb2gmx ended up with the warning WARNING: atom CG not found in residue 14 while adding atom and the error Fatal error: Atom CG not found in residue ASP14 while adding hydrogens Specifying -missing in pdb2gmx doesn't work. In the original PDB file, a few mis

Re: [gmx-users] How to define protein surface residues

Thanks, but what I mean is to just find out the surface residues, not to calculate the surface area. 2009/3/3 David van der Spoel > Lee Soin wrote: > >> Hello! >> I'm trying to find the surface residues of a protein. Maybe this should be >> calculated by myse

[gmx-users] How to define protein surface residues

Hello! I'm trying to find the surface residues of a protein. Maybe this should be calculated by myself and not using GROMACS. Can anybody tell me a feasible procedure for doing so? Thanks! -- Sun Li Department of Physics Nanjing University, China ___ gm

Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

ch I am not sure of its effect, is, perhaps, to take > extremely small cutoffs. > --Omer. > > > Lee Soin wrote: > > I'm trying to rule out the effect of electrostatic or Van der Waals > interactions while performing a simulation. Do you mean that I should modify > the c

Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

I'm trying to rule out the effect of electrostatic or Van der Waals interactions while performing a simulation. Do you mean that I should modify the code and re-compile? 2009/2/23 Justin A. Lemkul > > > Lee Soin wrote: > >> Hi! >> Is there an option to turn off e

[gmx-users] Turning off electrostatic or Van der Waals interactions

Hi! Is there an option to turn off electrostatic or Van der Waals interactions in GROMACS? -- Sun Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Pl

Re: [gmx-users] About position restraint specification

There's also an option "freezegrps". When should this be used? 2009/2/23 Justin A. Lemkul > > > Lee Soin wrote: > >> Hello, all! >> Which option in .mdp file is used to specify position restraint and the >> corresponding force constant? >> &g

[gmx-users] About position restraint specification

Hello, all! Which option in .mdp file is used to specify position restraint and the corresponding force constant? -- Sun Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailma

Re: [gmx-users] mdrun output conformation file loses chain identifier

Thanks! trjconv with -s works fine! 2009/1/19 Berk Hess > Hi, > > Are the two chains in a single molecule definition or in two molecule > definitions? > > There are no chain identifiers written in the tpr file. > But mdrun of Gromacs 4.0 will automatically generate chain identifiers for > each m

[gmx-users] mdrun output conformation file loses chain identifier

Hello! I'm using GROMACS to perform a double-chain MD simulation. It surprises me that the mdrun output conformation file ( specified by -c ) contains no more chain identifier ( A or B ) that exists in the original input PDB file. So can someone tell me how to re-integrate the chain identifier into

[gmx-users] About the -multi option in mdrun

Hello! How to specify the -multi option when doing REMD with mdrun? It seems that this option has changed from bool to int type in version 4.0. -- Sun Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] About REMD specification in mdrun argument

ng Ye <[EMAIL PROTECTED]> > each tpr contains only one temperature. > > On Tue, Dec 2, 2008 at 1:29 PM, Lee Soin <[EMAIL PROTECTED]> wrote: > > Hi, everyone! > > There's something that I'm not clear about REMD in gromacs. Since all the > > inputs are unifie

[gmx-users] About REMD specification in mdrun argument

Hi, everyone! There's something that I'm not clear about REMD in gromacs. Since all the inputs are unified into a unique .tpr file, why should the REMD options -multi and -replex be sprcified as mdrun arguments instead of being integrated into the same .tpr file? -- Sun Li Department of Physics N

Re: [gmx-users] mdrun doesn't run in version 4.0 on sgi server

]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src' make: *** [install-recursive] Error 1 My intel compiler versions are both 10.1.018. 2008/10/27 Mark Abr

Re: [gmx-users] mdrun doesn't run in version 4.0 on sgi server

By invoking "uname -a": Linux sgi4700 2.6.16.46-0.12-default #1 SMP Thu May 17 14:00:09 UTC 2007 ia64 ia64 ia64 GNU/Linux I don't know any other command to retrieve system information. 2008/10/27 Mark Abraham <[EMAIL PROTECTED]> > Lee Soin wrote: > >>

Re: [gmx-users] mdrun doesn't run in version 4.0 on sgi server

Everything works fine by setting NOASSEMBLYLOOPS. Thanks! 2008/10/26 Mark Abraham <[EMAIL PROTECTED]> > Lee Soin wrote: > >> Single CPU run. These are the last lines of the log file: >> > > Configuring nonbonded kernels... >> Testing ia64 CPU family...Unkno

Re: [gmx-users] mdrun doesn't run in version 4.0 on sgi server

-3690 --- Thank You --- 2008/10/26 Mark Abraham <[EMAIL PROTECTED]> > Lee Soin wrote: > >> Hello! >> I'm using gromacs 4.0 on an sgi server. Everything compiled OK. Every >> program in gromacs runs OK, except mdrun. Mdrun stops

[gmx-users] mdrun doesn't run in version 4.0 on sgi server

Hello! I'm using gromacs 4.0 on an sgi server. Everything compiled OK. Every program in gromacs runs OK, except mdrun. Mdrun stops every time at this point: Loaded with Money starting mdrun 'IMMUNOGLOBULIN G BINDING PROTEIN G in water' 10 steps,200.0 ps. Then nothing happens.The CPU usage

Re: [gmx-users] How to confine a protein in a box?

I'm going to put two peptide chains in a box and study dimerization. I think confining them in a box can reduce conformational search. 2008/10/14 Jochen Hub <[EMAIL PROTECTED]> > Lee Soin wrote: > > Hello, all! I intend to simulate a protein confined in a box. Can anybod

Re: [gmx-users] Simulation of a protein confined in a box

This seems to me a very complicated realization. Why doesn't GROMACS provide an easy way for wall simulation? 2008/10/11 Omer Markovitch <[EMAIL PROTECTED]> > Oh, I didn't read carefully. > My suggestion would be, perhaps, to physically put atoms on the sides of > the box (possibly, fill each sid

[gmx-users] Option -shuffle, -sort, -np missing in grompp in version 4.0?

The command grompp used to have options -shuffle, -sort and -np, but it seems that they appear no more with version 4.0? -- Sun Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

[gmx-users] How to confine a protein in a box?

Hello, all! I intend to simulate a protein confined in a box. Can anybody tell me how to define a boundary, or a wall, in GROMACS? Thanks! -- Sun Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Simulation of a protein confined in a box

itute of Science. > http://www.weizmann.ac.il/sb/faculty_pages/Levy/ > > > On Fri, Oct 10, 2008 at 11:03, Lee Soin <[EMAIL PROTECTED]> wrote: > >> But the problem is: how to define a boundary? >> > > > ___ > gmx-

Re: [gmx-users] Simulation of a protein confined in a box

But the problem is: how to define a boundary? 2008/10/10 Xavier Periole <[EMAIL PROTECTED]> > On Fri, 10 Oct 2008 15:09:31 +0800 > "Lee Soin" <[EMAIL PROTECTED]> wrote: > >> Hi! I'm going to simulate a protein confined in a box. Can GROMACS do &g

[gmx-users] Simulation of a protein confined in a box

Hi! I'm going to simulate a protein confined in a box. Can GROMACS do this? Will the removal of the periodic boundary condition be OK? -- Sun Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org http://w

[gmx-users] Simulation of a protein confined in a box

Hi! I'm going to simulate a protein confined in a box. Can GROMACS do this? Will the removal of the periodic boundary condition be OK? -- Sun Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org http://w

Re: [gmx-users] Can GROMACS mutate a residue?

7/12/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > > > > Lee Soin wrote: > >> Hi! > >> Is there a command in GROMACS that can substitute the atoms of a whole > >> residue for another? This is quite useful in doing mutation simulations. >

[gmx-users] Can GROMACS mutate a residue?

Hi! Is there a command in GROMACS that can substitute the atoms of a whole residue for another? This is quite useful in doing mutation simulations. Or if that's not possible, how should I mutate a residue? Thanks! -- Sun Li Department of Physics Nanjing University, China _

Re: [gmx-users] anyone knows how to install grace?

I also tried hard to install grace. Never succeeded. 2008/6/30 wang kelvin <[EMAIL PROTECTED]>: > Hi > > I want to use grace 5.1.9 (normally xmvgr). each time i do installation > using " ./configure", it prompts motif not found . > > So i tried to find free softare openmotif (it can do the same w

Re: [gmx-users] (no subject)

Hello, Venkatesh Hariharan! To perform AFM pull you should provide an additional input file named xxx.ppa and append "-pi xxx.ppa" to mdrun arguments. You can read GROMACS online or paper manual for detail. 2008/6/24 VENKATESH HARIHARAN <[EMAIL PROTECTED]>: > Hello, > > I am new to GROMACS, an

Re: [gmx-users] Does GROMACS have a multi-thread implementation?

Thanks! 2008/6/24 Carsten Kutzner <[EMAIL PROTECTED]>: > Lee Soin wrote: > >> But I see that in mdrun there's an option nt--number of threads to start >> on each node. Does this mean multi-thread? >> > Yes, nt means number of threads. It's alread

Re: [gmx-users] Does GROMACS have a multi-thread implementation?

But I see that in mdrun there's an option nt--number of threads to start on each node. Does this mean multi-thread? 2008/6/24 Carsten Kutzner <[EMAIL PROTECTED]>: > Lee Soin wrote: > >> Does GROMACS have a multi-thread implementation, instead of using MPI? >> > N

[gmx-users] Does GROMACS have a multi-thread implementation?

Does GROMACS have a multi-thread implementation, instead of using MPI? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please