RE: [gmx-users] electrostatics with non-periodic system

Hi, For pure water (no ions, no external electric field), reaction field does fine even with a short cut-off, e.g. 0.9 nm (use reaction-field-zero if you need good energy conservation). In case you have long-range fields, use no-cutoff at all (all cut-off to 0 in the mdp file) when you system

Re: [gmx-users] Query regarding protonation and deprotonation of some residues

Thanks Kass for the help. I want to specifically protonate one of the lysine near the active site and deprotonate Tyr and Ser. It will be kind if  you can please help me to know how to select that specific residue number. Regards -- Sonali Dhindwal --- On Mon, 27/9/10, Itamar Kass

[gmx-users] Re: A common error Atom O11 in residue bDM 1 was

OK you thank Justin for your explanation. Accordingly, I have changed the C* and O* atom names in the pdb and now it works. A bientôt Stefane ABEL Stephane 175950 wrote: You are right Justin, The 1O1 atoms and (others 1O2, etc.) are changed to O11, O21, etc. (?). Why this problem

Re: [gmx-users] Query regarding protonation and deprotonation of some residues

Hi Sonali, First of all, you'll have to find a force field that supports tyrosinate and serinate. These aren't generally considered titratable and are consequently not in the list for interactive selections with pdb2gmx. Once you've found a suitable force field, you'll have to set the protonation

Re: [gmx-users] Reg: Adding multiple molecules

vinothkumar mohanakrishnan wrote: Hi all I have a diffculty in adding multiple molecules of hexane to my box. my box size is 4.72*2.36*2.36 (nm) according to my number density calculations the box should fit 124 molecules of hexane whereas it adds only 76 molecules to the box below is my

Re: [gmx-users] How to make a lipid bilayer with specific dimensions?

NG HUI WEN wrote: Dear gmxusers, I am trying to make a lipid bilayer with specific dimensions using gromacs. So far, I have got up to: 1) Download a lipid POPC128a.pdb from Peter Tieleman’s website 2) Use genconf –f popc128a.pdb –o popcx2.pdb –nbox 2 2 1 to multiply

[gmx-users] Re: Ask for a question

Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. Most of your questions can be answered by reading molecular modeling textbooks or review articles about pulling. Some of this information is also in the manual, so you've certainly missed it.

Re: [gmx-users] Reg: Adding multiple molecules

Hi justin if genbox is not able to find sufficient space then why should one calculate number density for the given box dimension?.similarly the the number of molecules are not getting updated in the molecules section of the topology file when inserting multiple molecules using the genbox

Re: [gmx-users] Reg: Adding multiple molecules

vinothkumar mohanakrishnan wrote: Hi justin if genbox is not able to find sufficient space then why should one calculate number density for the given box dimension?.similarly the the Just because you can calculate a certain number density does not necessarily mean that the algorithm

[gmx-users] Pulling Simulation Query

Hi ... Just wondering if there's a way, during pulling simulations, to immobilise say the C-terminus of the protein. I've been running through the 'Umbrella Sampling' tutorial with my own protein. Within this tutorial the ChainB is used as the immobile reference - so it is this that is

Re: [gmx-users] Reg: Adding multiple molecules

Hi Justin Thank you for your suggestion. Regards Vinoth On Mon, Sep 27, 2010 at 4:52 PM, Justin A. Lemkul jalem...@vt.edu wrote: vinothkumar mohanakrishnan wrote: Hi justin if genbox is not able to find sufficient space then why should one calculate number density for the given box

[gmx-users] How to make a lipid bilayer with specific dimensions?

I don't think that this is currently causing anybody any problems, but note that genbox is going to cut any lipids that cross out of the central unit box (either because genbox is unaware of PBC or because these lipids now clash across PBC). Therefore: genbox -cs popc128a.pdb -o

[gmx-users] Salt concentration

Dear Users: I am interested in perform a simulation of a protein in different salt concentrations. How I can calculate how much Na+ and Cl- ions to include in the simulation to achieve certain concentration? Could someone point me in the right direction? Is there a software to do this type of

Re: [gmx-users] Salt concentration

Hi Anthony, You can use the '-conc' tag from genion during file preparation, as per http://manual.gromacs.org/current/online/genion.html. Gonçalo On 27 September 2010 15:32, Anthony Cruz Balberdi anthony.cr...@upr.eduwrote: Dear Users: I am interested in perform a simulation of a protein in

[gmx-users] LJ potential

Hello, Is there a way to turn off the 6-term in LJ 6-12 potential? -Nisha P. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't

Re: [gmx-users] LJ potential

On 2010-09-27 18.37, nishap.pa...@utoronto.ca wrote: Hello, Is there a way to turn off the 6-term in LJ 6-12 potential? -Nisha P. Set the parameters to zero? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden.

[gmx-users] (no subject)

Dear users of GROMACS, I have a problem with force field . Can you tell me what other ff except OPLS-AA I can use for Al3+ or other trivalent ions ? Thank you Mira -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] LJ potential

How can I do that using OPLSAA, because in the nb.itp file the values are for sigma/epsilon? Can I change C6=0 in the code file? Quoting David van der Spoel sp...@xray.bmc.uu.se: On 2010-09-27 18.37, nishap.pa...@utoronto.ca wrote: Hello, Is there a way to turn off the 6-term in LJ 6-12

[gmx-users] MPI and dual-core laptop

Hi, I wanted to test the GROMACS MPI version in my dual-processors laptop. I have installed openmpi 1.4.2 version. However, when I tried to configure GROMACS 4.5.1 with --enable-mpi option, I got the following configuration problem: checking whether the MPI cc command works... configure: error:

Re: [gmx-users] MPI and dual-core laptop

Hi, My 2 cents on your problem: I've been running gromacs on nearly everything, from one to six cores. It works. Besides mpi being in your /usr/local/bin, is it on the path of your system? You can do, in the terminal export PATH=$PATH:/usr/local/bin Or, for a more permanent solution, go to

[gmx-users] g_hbond segmentation fault

-- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915Segmentation fault __ Hi guys, I got the msg like above when

Re: [gmx-users] Tables with forcefield

Thanks M! I am using the standard 6-12 tables available with the gromacs package. For -table and -tablep options to start with. I want to understand 1 thing. The forcefield files and the topology file specifies sigma and epsilon parameters. If I change the combination rule to 1 in the

Re: [gmx-users] g_hbond segmentation fault

Yao Yao skrev 2010-09-27 21.22: -- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915Segmentation fault __ Hi

[gmx-users] Hardware-specific crash with 4.5.1

Hi All, I'm hoping I might get some tips in tracking down the source of an issue that appears to be hardware-specific, leading to crashes in my system. The failures are occurring on our supercomputer (Mac OSX 10.3, PowerPC). Running the same .tpr file on my laptop (Mac OSX 10.5.8, Intel

RE: [gmx-users] Salt concentration

Calculator or spreadsheet will do the job fine. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9909 9304 - When the

[gmx-users] Gromacs 4.0.7 failing in parallel mode

Hi, I am simulating two protein units in water and it works fine in the single processor but when I use the parallel version of the GROMACS, it fails. My script: grompp_mpi_d -f md.mdp -c hba_b4md.gro -r hba_b4md.gro -p hba.top -o hba_md.tpr mpirun -np $NPROCS mdrun_mpi_d -np $NPROCS

Re: [gmx-users] Gromacs 4.0.7 failing in parallel mode

- Original Message - From: Jyoti Mahalik jmaha...@polysci.umass.edu Date: Tuesday, September 28, 2010 9:19 Subject: [gmx-users] Gromacs 4.0.7 failing in parallel mode To: gmx-users@gromacs.org Hi, I am simulating two protein units in water and it works fine in the single processor

Re: [gmx-users] Hardware-specific crash with 4.5.1

Justin, I think the interaction kernel is not OK on your PowerPC machine. I assume that from: 1) The force seems to be zero (minimization output). 2) When you use the all-to-all kernel which is not available for the powerpc kernel, it automatically falls back to the C kernel and then it works.

[gmx-users] Psuedo ONIOM gromacs MD run

Hello all, Is it possible to do a pseudo ONIOM MD run where you hold all atoms rigid except for a small sphere of some radius. I was wondering if I could do this with posres.itp files or a define argument. It would be beneficial if the atoms held rigid had no

Re: [gmx-users] Psuedo ONIOM gromacs MD run

Freeze groups do something along these lines. See manual. Mark - Original Message - From: TJ Mustard musta...@onid.orst.edu Date: Tuesday, September 28, 2010 10:46 Subject: [gmx-users] Psuedo ONIOM gromacs MD run To: gmx-users@gromacs.org gmx-users@gromacs.org

Re: [gmx-users] Hardware-specific crash with 4.5.1

Roland Schulz wrote: Justin, I think the interaction kernel is not OK on your PowerPC machine. I assume that from: 1) The force seems to be zero (minimization output). 2) When you use the all-to-all kernel which is not available for the powerpc kernel, it automatically falls back to the C

[gmx-users] Another error that keeps comming up.

Hey all, Here is another error that I keep getting. I am trying to speed up my md runs with -heavyh and longer time steps. I dont get LINCS errors but I do get this... Back Off! I just backed up prlog.log to ./#prlog.log.1# Getting Loaded...

Re: [gmx-users] Hardware-specific crash with 4.5.1

Mark Abraham wrote: - Original Message - From: Justin A. Lemkul jalem...@vt.edu Date: Tuesday, September 28, 2010 11:11 Subject: Re: [gmx-users] Hardware-specific crash with 4.5.1 To: Gromacs Users' List gmx-users@gromacs.org Roland Schulz wrote: Justin, I think the

RE: [gmx-users] How to make a lipid bilayer with specific dimensions?

Thanks for that guys! I will try them out. Just a quick question here with regards to my lipids being possibly too small, does it have something to do with the minimum image criterion for PBC? I have ensured that the distance of edge of the box and the atoms at the side of the protein to be

Re: [gmx-users] How to make a lipid bilayer with specific dimensions?

NG HUI WEN wrote: Thanks for that guys! I will try them out. Just a quick question here with regards to my lipids being possibly too small, does it have something to do with the minimum image criterion for PBC? I have ensured that the distance of edge of the box and the atoms at the side of

RE: [gmx-users] How to make a lipid bilayer with specific dimensions?

Points noted, thanks Justin! -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Tuesday, September 28, 2010 10:06 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to make a lipid bilayer

Re: [gmx-users] Compilation error - GROMACS 4.5.1

- Original Message - From: Shachi Katira sha...@berkeley.edu Date: Tuesday, September 28, 2010 12:56 Subject: [gmx-users] Compilation error - GROMACS 4.5.1 To: gmx-users@gromacs.org Hi all, I get the following errors when I try to compile the double precision version of GROMACS

Re: [gmx-users] Hardware-specific crash with 4.5.1

On Mon, Sep 27, 2010 at 9:58 PM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Justin A. Lemkul jalem...@vt.edu Date: Tuesday, September 28, 2010 11:39 Subject: Re: [gmx-users] Hardware-specific crash with 4.5.1 To: Discussion list for GROMACS users