Re: [gmx-users] problems with nsgrid

The previous e-mail refers to simulation running with mdrun in double precision, using the single precision the problem is disappered. Regards Gianfranco - Original Message - From: "Gianfranco Bocchinfuso" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Tuesday, Fe

[gmx-users] Re: Re: trjconv and missing chain identifier

Mark Hi Mark and other users, Thanks for your reply and apologies for my English. If the chain identifiers are discarded by gromacs why do I than get from trjconv an output file looking like this when having more than one chain in the .trr file like in this example (part of .pdb file) ATOM

Re: [gmx-users] Re: Re: trjconv and missing chain identifier

Hi Una, You can do it in pymol (http://pymol.sourceforge.org/): alter i. x-y, chain="Z" where x is the first residue number and y the last of the chain you want to give an identifier, and Z is the one-letter chain id. You can afterwards write the .pdb file again, with the chain ids, but you ha

Re: [gmx-users] Re: Re: trjconv and missing chain identifier

> Mark > > Hi Mark and other users, > > Thanks for your reply and apologies for my English. > > If the chain identifiers are discarded by gromacs why do I than get > from trjconv an output file looking like this when having more than one > chain in the .trr file like in this example (part of .pdb

[gmx-users] g_bond -hx

Hi. I used g_hbond with -hx option, to study intramolecular bonding in my polymer (a poly(vinyl alcohol) partially hydrophobized with metacrylate groups). I found a quite high number of hydrogen bonds between n-n residues. What does a HB between n-n residues represent? A intra-residue HB? I hav

[gmx-users] Protein Dipole moment

Hello Does g_dipole take the center of mass of a molecule as the origin when calculates its dipole moment? If yes, is it the com at t=0 that is used or is it re-calculated for every frame? I had look at the source code but it wasn't very clear to me. Thank you very much in advance. Best wis

[gmx-users] Re: Carbon nanotube force field

[EMAIL PROTECTED] wrote: Dear Prof. Dr. Van der Spoel, I'm simulating a system involving carbon nanotubes. As an initial test of my force field I want to simulate a single carbon nanotube. I've done simulations at constant volume and constant pressure. However, it seems that the energy is alway

[gmx-users] Inconsistent shifts using multiple bonds type 6

Hello all, I am trying to apply a set of harmonic distance restraints between pairs of protein atoms in my system, which is protein/ligand/water/ions in a periodic box. The way i am doing this is to use the bond type 6 and to add these bonds at the end of the [bonds] section in my topology f

[gmx-users] Frozen atoms and energy group exclusion

Hello, I asked a similar question to this a bit ago, but didn't get much of a response. I have a lipid bilayer system of 128 DPPC molecules in water. I want to fix the bottom face of the bilayer, and I am doing so by freezing the positions of the first 12 atoms of the DPPC molecule. The man

Re: [gmx-users] Inconsistent shifts using multiple bonds type 6

> Hello all, > > I am trying to apply a set of harmonic distance restraints between pairs > of > protein atoms in my system, which is protein/ligand/water/ions in a > periodic box. > > The way i am doing this is to use the bond type 6 and to add these bonds > at > the end of the [bonds] section in

Re: [gmx-users] Frozen atoms and energy group exclusion

> When I run this through grompp, I get the following error: > WARNING 1 [file "dppc.top", line 19]: > Can not exclude the lattice Coulomb energy between energy groups > Checking consistency between energy and charge groups... > --- > Progr

Re: [gmx-users] grompp error in peptide-membrane simulations

Hi Tsjerk: thanks again for the full description of what i should to do. I did it and grompp runs ! cheers Maite On 3/3/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: Hi Maite, Indeed you shouldn't really run the lipids through pdb2gmx, but try to obtain a .itp file for a lipid, match

Re: [gmx-users] Inconsistent shifts using multiple bonds type 6

Hi Mark thanks for your reply, I'm not sure the problem is that these restraints are inappropriate, but the problem might be the sheer number. For example if i restrain a fairly large number of atom distances (say 100 Calpha distances) to the same length they are in the structure after minimis

[gmx-users] Re:realloc Error !

Mark: Thank you for your advice,I always get one of these error message, in same situation. I find that when I got box shift error message,there are many lincs warning. I did not find some special message for memory not enough error message. > Qiang Zhong : > > I have a complex protein

Re: [gmx-users] Frozen atoms and energy group exclusion

Hello, Thanks for the fast response. I went through my dppc.itp file and chose atoms such that the group of frozen atoms has a net charge of 0 as does the rest of the molecule. When running this through grompp, the error before about the atoms being in different charge groups is gone. Howev

[gmx-users] g_density : centering the density distribution plot

Hello, I'd like to use g_density to obtain a density distribution plot. Now, I'd like to place the center of that distribution on the zero of the horizontal axis. How do I so using g_density? From reading the manual, I see there's an option, "-center", which should do the trick. But I've

[gmx-users] vacuum right but melt collapse

Hi GMX user: A model for Poly(vinyl methyl ether) was built with OPLS force field ( all H ). When the model was run alone (a single chain) in vacuum, anything goes ok. But with 45 chains box, the system will be collapse with a little bond elongates abnormal whatever in NVT or NPT. Th

Re: [gmx-users] vacuum right but melt collapse

kitty ji wrote: > Hi GMX user: > > A model for Poly(vinyl methyl ether) was built with OPLS force field ( > all H ). > > > > When the model was run alone (a single chain) in vacuum, anything goes ok. > > > > But with 45 chains box, the system will be collapse with a little bond > elongat

[gmx-users] .GRO and .TOP files editing

I have a polymer molecule (non-protein). Therefore I could not use pdb2gmx and I tried to use PRODRG, but it could process only small molecule. I was suggested to run PRODRG with small molecule and manually stich the top file. Therefore I used a small molecule and obtained the .gro and .top files

[gmx-users] Mac OS X with MKL

Hi Gromacs folks, I'm trying to build Gromacs with MKL on Mac OS X. I am running the configuration with: ./configure --prefix=/Users/wyuen/west/gromacs/gromacs_icc64 --enable- mpi --enable-float --with-fft=mkl But I am getting the following error: checking for mkl_dfti.h... yes checking for