[gmx-users] bug in function read_next_vmd_frame

Hi, there: It seems to me that there was a bug at line 214 of function read_next_vmd_frame() in file ./src/gmxlib/vmdio.c. vec[0] = .1*ts.A; vec[1] = .1*ts.B; vec[2] = .1*ts.B; should be changed to : vec[0] = .1*ts.A; vec[1] = .1*ts.B; vec[2] = .1*ts.C; This is identified in gromacs4.5.1 ve

[gmx-users] residue IDs are not ordered in gro file.

Hi, there: I found that in gromacs version 4.5.1, the residue ids are not ordered consecutively as before in the .gro file. For example, if I have two chains in the protein, then the residue ids will be ordered with respect to each individual chain, rather than reordered to be a complete

Re: [gmx-users] residue IDs are not ordered in gro file.

Dear Justin: Thanks a lot for your reply. I indeed have missing residues in the second chain. However, when I try pdb2gmx -renum, it renumbers the second chain starting from 1, rather than starting from 817(Nres_1st+1). Thanks, Bin = 816VAL HG131

[gmx-users] compiling gromacs4.5 with gpu

Hi, there: I was trying to compile gromacs4.5.1 on a GPU cluster (https://secure.nersc.gov/nusers/systems/dirac/ ). The compilation seems to work fine, but in the installation folder, only "bin/mdrun-gpu" presents. Is it supposed to be so? When I type "./mdrun-gpu -h", the following error

Re: [gmx-users] compiling gromacs4.5 with gpu

BUILD_SHARED_LIBS and or you can ran "make install" as a workaround until the bug is fixed. Roland On Tue, Sep 28, 2010 at 3:02 AM, BIN ZHANG wrote: Hi, there: I was trying to compile gromacs4.5.1 on a GPU cluster (https://secure.nersc.gov/nusers/systems/dirac/ ). The compilation see

[gmx-users] charmm27 force filed bug for MET residue with vsites in gromacs 4.5.2

Dear all: I used gromacs 4.5.2 to generate the topology for a small protein with charmm27. pdb2gmx_mpi -f 1PIN.pdb -o protein.gro -vsite hydrogen -his -ignh -ter -p topol -nochargegrp When I try to use the topology in grompp, the following error appeared: Fatal error: Can't do GB electrosta

[gmx-users] tpbconv -zeroq results all coulombic energies to zero

Hi, all: I was trying to use "tpbconv" to modify the tpr file with the command: tpbconv -s %s.tpr -nsteps -1 -zeroq -n index -o final.tpr It basically sets the charge of one group to zero. However, when I perform mdrun -rerun, all the coulombic energies are zeros, i.e., Coulomb-(SR), Coul.-r

[gmx-users] Re:Re: tpbconv -zeroq results all coulombic energies to zero

rotein and none of them give me sensible results (the charges are not all set to zero). Is this supposed to be a bug? Thanks, Bin On 2010-12-03 08.45, BIN ZHANG wrote: Hi, all: I was trying to use "tpbconv" to modify the tpr file with the command: tpbconv -s %s.tpr -nsteps -

[gmx-users] mix berger ff with opls

Dear all: I was trying to convert the lipid.itp downloaded from Tieleman's website to the format compatible with OPLS. I basically followed the procedure in this post, which is really helpful: http://www.mail-archive.com/gmx-users@gromacs.org/msg03459.html But there is one comment there I d

Re: [gmx-users] mix berger ff with opls

Dear Chris: Thanks a lot for your reply. That's really helpful. Now I have a further question: "1,4 electrostatic inter-actions were reduced a factor of 2 and 1,4 Lennard?Jones interactions a factor of 8." I can understand that the LJ1-4 can be reduced by simply scale epsilon in [pairty

Re: [gmx-users] mix berger ff with opls

Dear Chris: Now it makes all sense. Thanks a lot. And your method surly works great. Bin On Mar 15, 2010, at 9:23 AM, chris.ne...@utoronto.ca wrote: Dear Bin, I think that you are getting confused here between different publications. It was the Lindahl, E., and O. Edholm. 2000. paper tha

[gmx-users] gromacs 4.0 on CRAY-XT4

Dear all: I was trying to build gromacs 4.0 on a cray-xt4 machine, the same one as the benchmark in the gromacs4 paper (). However, my timing for a similar system, ~100,000 atoms, is almost 3 times slower than in the paper. For example, I only got ~25 ns/day with 128 cpus. So is there any

Re: [gmx-users] gromacs 4.0 on CRAY-XT4

protein and I'm using berger lipid/OPLS-AA force filed. Thanks Bin On Mar 17, 2010, at 12:02 AM, Mark Abraham wrote: On 17/03/2010 5:43 PM, BIN ZHANG wrote: Dear all: I was trying to build gromacs 4.0 on a cray-xt4 machine, the same one as the benchmark in the gromacs4 paper (). Howe

Re: [gmx-users] gromacs 4.0 on CRAY-XT4

benckmark, on a cray-xt4 machine. Here is also a link for the machine I'm working on: http://www.nersc.gov/nusers/systems/franklin/ Bin. On Mar 17, 2010, at 1:39 AM, Roland Schulz wrote: On Wed, Mar 17, 2010 at 3:55 AM, Mark Abraham wrote: On 17/03/2010 6:19 PM, BIN ZHANG wrote:

Re: [gmx-users] gromacs 4.0 on CRAY-XT4

(there were problems with Gromacs and PGI before). Roland On Wed, Mar 17, 2010 at 1:27 PM, BIN ZHANG wrote: Dear mark, and Roland: Thanks for all the suggestions. I was confused gromacs4 paper with another one by Erik Lindahl. (http://www.ncbi.nlm.nih.gov/pubmed/19229308 ) Since there the

[gmx-users] output forces between group of atoms

Dear all: In gromacs, is it possible to output forces between two groups of atoms? Or is it possible to decompose forces into separate parts, like for LJ, and electrostatics? Thanks, Bin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] output forces between group of atoms

Dear Mark: Thanks a lot for all the suggestions. They are really illuminating. Sincerely, Bin On Mar 26, 2010, at 5:56 PM, Mark Abraham wrote: On 27/03/2010 8:24 AM, BIN ZHANG wrote: Dear all: In gromacs, is it possible to output forces between two groups of atoms? Yes. Run a

[gmx-users] coarse grain in gromacs

Hi, all: Has anyone done the coarse graining using MARTINI force field? Could you give me any suggestion on how to build a coarse grained model from the AA system? I checked the website(http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html ) and it seems to me they only provide a scrip

Re: [gmx-users] coarse grain in gromacs

? Thanks in advance. Bin On Nov 24, 2008, at 1:32 AM, Xavier Periole wrote: On Sun, 23 Nov 2008 21:48:52 -0800 BIN ZHANG <[EMAIL PROTECTED]> wrote: Hi, all: Has anyone done the coarse graining using MARTINI force field? Could you give me any suggestion on how to build a

[gmx-users] CGMD timestep

Dear all: Has anyone tried to run a NVE simulation for the coarse grained dynamics using MARTINI force field? It's a little weird to me that 1fs/ step needs to be used to conserve the energy when protein is present in the system. Does this make sense? Thanks a lot. Bin --

[gmx-users] two reference groups in pull code

Dear all: Reading about the gromacs4 manual, I couldn't figure out a way to apply two sets of pulling simultaneously in gromacs? I know you can specify a second group using pull_group2, but it has to use the same reference group in pull_group0, correct? Then I don't understand how one can a

Re: [gmx-users] two reference groups in pull code

Dear Chris: Thanks very much for the info. I will take a look at the source code and see how far I can go.;-) Bin On Apr 9, 2010, at 11:38 AM, chris.ne...@utoronto.ca wrote: Dear Bin: What you request is not currently possible with any distribution up to gmx-4.0.7 (I don't know if it is i

[gmx-users] python wrapper from libxdr?

Dear all: I found this really interesting email on the mail list about the python wrapper for the xdrfile library: http://oldwww.gromacs.org/pipermail/gmx-developers/2009-March/003176.html But unfortunately the link for the python files are not valid anymore. I am wondering whether this proj

[gmx-users] Re: python wrapper from libxdr?

downloaded from the GROMACS website: http://www.gromacs.org/index.php?title=Download_%26_Installation Roland On Mon, May 10, 2010 at 1:42 PM, BIN ZHANG wrote: Dear all: I found this really interesting email on the mail list about the python wrapper for the xdrfile library: http

[gmx-users] implicit solvent in CVS

Dear all: I know this question has been asked many times, but it's still tempting for me to ask it again ;-). Could any one suggest a mdp file, including the proper parameter setting, for implicit solvent simulation in gromacs? From all the clues I gathered (the roadmap, the source code),

[gmx-users] converting amber parameter to OPLS

Dear all: I'm considering to convert the ATP/ADP parameters from amber (http://www.pharmacy.manchester.ac.uk/bryce/amber ) into OPLS format. My question is, have you guys done similar things? If so, can you give me some information on what kind of thing I should be aware of? Like the scaling

Re: [gmx-users] OPLS-AA topologies for ATP

Hi, I recently made up a topology for ADP. You can probably modify it to ATP easily. I used native OPLS atom types based on the DNA parameters (http://rnp-group.genebee.msu.su/3d/ff.htm ). The charges are copied from CHARMM27. Also, there is one dihedral angle missing, again, copied from CHA

Re: [gmx-users] OPLS-AA topologies for ATP

yce/amber#cof However, I would also ask is there a specific reason you wish to use OPLS-AA/L? If not then it is probably easier to use one of the AMBER forcefields with these parameters as you do not need to do any testing (or wait for me to publish my work!) Cheers Tom BIN ZHANG wrote:

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

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

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

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