[gmx-users] Free energy of solvation of large molecule

Hi, I'm trying to calculate the free energy of solvation of a relatively large polymer molecule (161 atoms). I went through the free energy tutorial published on J. Lemkul's web page but when trying to apply the same approach to my case, the simulations typically fail. The files for one such case

[gmx-users] Re:On the usage of g_sas

no word about the naming conventions. Even ol' fella Google can't find anything related to this issue. Best, Jernej > On 10/8/13 7:27 AM, Jernej Zidar wrote: >> Hi, >>I would like to use g_sas to determine the surface properties of an >> organic molecule

[gmx-users] On the usage of g_sas

option is better? I'm using the Charmm-generalized forcefield. Thanks in advance for the advice, Jernej Zidar -- Windows: Re-Boot, Linux: Be-Root. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

[gmx-users] Re: Problem running free energy simulations

Dear Michael. The simulations at each lambda point starts from the same structure that I equilibrated (NPT ensemble) for 20 nanoseconds. The system has ~7500 atoms in a box the size 5 nm x 5 nm x 5 nm. The molecule of interest is located in the center of the unit cell. Thanks, JErnej > > Sounds

[gmx-users] Problem running free energy simulations

Hi all, I'm trying to determine the free energy of solvation for a molecule in n-octanol. I'm separately turning off the Coulomb and Lennard-Jones interactions as instructed in the free energy tutorial. The Lennard-Jones simulations keep on crashing for most values of lambda with the message: Pro

[gmx-users] Re: gmx-users Digest, Vol 113, Issue 81

Re: [gmx-users] BGQ compilation with verlet kernels: #include file"kernel_impl.h" not found. Side note: On a Blue Gene/Q machine this particular version of Gromacs is 2.5x times faster than the regular one. I really hope thw BGQ accelerated kernels will go into the main branch soon.

[gmx-users] Re: MD vs. free energy simulations

cut-off. What can I do to remedy this? Thanks in advance, Jernej On 4. sep. 2013, at 09:55, Jernej Zidar wrote: > >> On 9/2/13 9:43 PM, Jernej Zidar wrote: >>> Dear Justin, >>> I set the couple_intramol parameter to yes and rerun the free energy >>>

[gmx-users] Re: MD vs. free energy simulations

> On 9/2/13 9:43 PM, Jernej Zidar wrote: >> Dear Justin, >> I set the couple_intramol parameter to yes and rerun the free energy >> simulations. mdrun was able to fully utilize all the cores in the >> system but there's one issue. The free energy of solvati

[gmx-users] Re: MD vs. free energy simulations

ar non-bonded interactions might lead to kinetically trapped vacuum conformations. The 1-4 pair interactions are not turned off." My molecule has 161 atoms. How large is "relatively large" ? Thanks in advance, Jernej Zidar On Thu, Aug 29, 2013 at 8:00 PM, wrote: > This issue is

[gmx-users] MD vs. free energy simulations

can I use more CPUs for 'regular' MD but only two for free energy simulations? I'd really like to use more CPUs as it would really speed-up the simulations. Thanks in advance, Jernej Zidar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/lis

[gmx-users] Re: Running g_tune_pme on a BlueGene/Q cluster

Hello, I tried as you suggested but the utility still fails. The job output file contains a myriad of errors like this: Program g_tune_pme, VERSION 4.6.3 Source code file: /home/ihpczidj/scratch/gromacs-4.6.3/src/tools/gmx_tune_pme.c, line: 665 Fatal error: Output from test run could not be foun

[gmx-users] Running g_tune_pme on a BlueGene/Q cluster

Hi, I would like to determine the optimum number of PP/PME nodes to be used for my simulation. I found the tool g_tune_pme can be used. The cluster is a BlueGene/Q machine using SLUR as the scheduler. I tried using the following scirpt: !/bin/bash #SBATCH --time=1:00:00 #SBATCH --nodes=16 #SBAT

[gmx-users] Gromacs: GPU detection

Hi there. Lately I've been running simulations using GPUs on a computer node. I noticed that though the GPUs are always in use sometimes I don't get this message in the output: Using 4 MPI threads Using 2 OpenMP threads per tMPI thread 4 GPUs detected: #0: NVIDIA Tesla C2070, compute cap.: 2.0

[gmx-users] [solved] Problem compiling Gromacs 4.6 on BlueGene/Q

>> >> 1. Compile FFTW-3.3.2: >> ./configure --prefix=/scratch/home/user/fftw-3.3.2 >> make && make install >> > > This does not compile a single-precision FFTW (per generic GROMACS > installation instructions). Hi Mark, Thanks for pointing it out. I recompiled FFTW like so: ./configure --prefix=

[gmx-users] Problem compiling Gromacs 4.6 on BlueGene/Q

Hi, I'm trying to compile Gromacs 4.6 on a BlueGene cluster but I've stumbled upon something that looks like a bug. Here's how I'm trying: 1. Compile FFTW-3.3.2: ./configure --prefix=/scratch/home/user/fftw-3.3.2 make && make install 2. Compile Gromacs 4.6 using instructions from Gromacs' pag

[gmx-users] Compiling GROMACS w CUDA 5.0 problem

Hi, I want to compile GROMACS to support CUDA. First I do a cmake: CMAKE_PREFIX_PATH=/scratch/ihpc/ihpczidj/local/bin/:/usr/local/CUDA/5.0/ cmake ../gromacs-4.6 -DGMX_GPU=ON -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF -DGMX_OPENMP=ON -DBUILD_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=/scratch/ihpc/ihpczidj/

[gmx-users] Problem importing PDB to Gromacs

Hi, In CHARMM I generated a short peptide. The N-terminal is a regular -NH2 (patch NNEU) while the C-terminal is amidated (patch CT2). I would like to import the PDB to GROMACS using pdb2gmx by using the CHARMM27 forcefield later. I issue the following command: pdb2gmx -v -f irik-l.pdb -inte

[gmx-users] g_enemat problem & suggestion

g_energy states all the groups missing by g_enemat are present in the energy file: 45 Coul-SR:unit1-unit1 46 LJ-SR:unit1-unit1 47 Coul-14:unit1-unit1 48 LJ-14:unit1-unit1 49 Coul-SR:unit1-unit2 50 LJ-SR:unit1-unit2 51 Coul-14:unit1-unit2

[gmx-users] g_enemat problem & suggestion

nytime soon. Also, I don't have any particular application now for the program ;-{" ( http://lists.gromacs.org/pipermail/gmx-users/2003-February/004123.html). Is g_enemat really broken? Or am I missing a detail or two not mentioned in the manual? thanks in advance for any explanation, J

[gmx-users] Differing data estimates between Gromacs versions - why?

I get the same estimate (huge) estimate whether I use the the binaries I compiled myself (w/o openMPI) or the ones present in the Ubuntu (12.04) repository. What could account for this difference? Thanks in advance, Jernej Zidar -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Simulation problem

comm-grps = POLYMER Water_CL_NA - - - Thanks in advance for any help or advice, Jernej Zidar -- 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

[gmx-users] Reordering of a large GRO file - how

cussion list for GROMACS users > Message-ID: <50eea589.4030...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > On 1/10/13 4:50 AM, Jernej Zidar wrote: >> Hi. >> I used editconf to replicate a small lipid bilayer patch, after >> edi

[gmx-users] Reordering of a large GRO file - how

34345 B 25 SOL 1 A 34345 B 25 SOL 1 ... Thanks in advance, Jernej Zidar -- 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'

[gmx-users] Re: gmx-users Digest, Vol 102, Issue 6

Hi. Thanks for the tip. I turned the problem was caused by the PDB file. It seems the water segment was not written properly (starting with residue 1 and then all the way to the last one). After correcting this and then manually editing the new PDB file to change the atom names from TIP3 to SPCE

Re: [gmx-users] Position restraints problem

True. Even more so if the position restraints file can be generated with basic Bash commands in under a minute. Jernej On 28. mar. 2012, at 20:16, gmx-users-requ...@gromacs.org wrote: > It's pretty rare to have more than a handful of [moleculetype] sections, > each of which would want customiz

[gmx-users] Position restraints problem

in turn means genrestr is useless if one has more than one molecule type. While I could set the restraints manually, doing it by hand is not really an option if one has more than 100 entries. Ah well, bash magic to the rescue. Thanks, Jernej Zidar For posterity reasons here's the warning: WA

[gmx-users] Position restraints problem

omacs.org/Documentation/Errors Indeed, checking the lipid ITP file revealed there is no atom index 12014, yet there is an atom index 12014 (with the proper name) in the GRO file (that I used to create both the index and the restraints file) where all the atoms are listed. What have I done wrong? Th

[gmx-users] Re: Problem: pdb2gmx with a more complex system

Dear Mark and Justin, Thank you for the clarification. Running the pdb2gmx with the following switches was enough to get a working topology file: pdb2gmx -v -f sys9-tmp.pdb -water spc -noter -o sys9-tmp.gro -p sys9-tmp.top -i sys9-tmp.itp -renum The resulting topology file is very simple: ; In

[gmx-users] Problem: pdb2gmx with a more complex system

cules work perfectly within CHARMM, but then again CHARMM has a different modus operandi. Thanks in advance for any help, Jernej Zidar -- 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/

[gmx-users] re: Unreadable trajectory [solved]

se the GRO file from the previous run. > > Don't, you're losing precision and introducing perturbations. grompp -t > old.cpt is your friend. > > Mark Using that. Many many thanks! Thanks for the help, Jernej Zidar -- gmx-users mailing listgmx-users@gromacs.org http://

[gmx-users] Unreadable trajetory

6/wpoly-2x-box-ions-nvt-nofix-2.log - TPR: http://dl.dropbox.com/u/5761806/wpoly-2x-box-ions-nvt-nofix-2.tpr I use GROMACS 4.5.5, the system is electrically neutral. To prepare a new TPR file a use the GRO file from the previous run. Thanks in advance for any tip, Jernej Zidar -- gmx-users mailing

[gmx-users] [solved] Using CHARMM force fields in Gromacs, pt. 2

@Peter C. Lai: I did like you suggested and now the two forcefields work in tandem as expected. @Mark Abraham: Thank you for the explanation. Best. Jernej Zidar On Mon, Feb 20, 2012 at 15:27, wrote: >> >>   There's no need to patch the forcefields.dat file because Grom

[gmx-users] Re: Using CHARMM force fields in Gromacs, pt. 2

h the forcefields.dat file because Gromacs will first look for the forcefields in /opt/share/gromacs/top/ and later in the local directory. Thanks again, Jernej Zidar On Mon, Feb 20, 2012 at 14:31, wrote: > Make a copy of the original Charm36.ff (to say, charmm36cgen.ff) then patch > your cgenff conv

[gmx-users] Using CHARMM force fields in Gromacs, pt. 2

ether in one simulation? Thanks in advance, Jernej Zidar -- 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 post (un)subscribe request

[gmx-users] Adding new residues and pdb2gmx

he LPPC residue is present in both the ./residuetypes.dat and ./charmm36/lipids.rtp files. What's wrong? I would really like to increase the verbosity of the pdb2gmx command but it seems the "-v" switch has no/little effect. Thanks in advance, Jernej Zidar -- gmx-users mailing list

[gmx-users] [~solved] Force field for polymer molecule - tips

Dear all, In December 2011 I was asking about tips on how to port a Charmm generalized forcefield for a polymer to Gromacs. I am happy to report that the forcefield was ported to Gromacs in a way that allows the use of pdb2mx in order to create an initial topology and .gro file. Major lesso

[gmx-users] Re: gmx-users Digest, Vol 92, Issue 73

rs (3 + 2 terminal ones), that are quite similar so after importing one I should be OK. Best, Jernej On Wed, Dec 14, 2011 at 12:17, wrote: > Jernej Zidar wrote: >> Hi Mark. >>>> How will pdb2gmx "know" it has to parse the monomeres.rtp file? >>> It

[gmx-users] Re: Force field for polymer molecule - tips (Mark Abraham)

Hi Mark. >> How will pdb2gmx "know" it has to parse the monomeres.rtp file? >It can't. You must add to an existing .rtp file. That's a problem (and a negative surprise), because I can't just add a new residue to the aminoacids.rtp in Charmm27.ff folder. Charmm27 and CGenFF are two different things

[gmx-users] Force field for polymer molecule - tips

r the only package that can generate the initial structures from a set of internal coordinates in the force field. Thanks in advance, Jernej Zidar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.o

[gmx-users] Using CHARMM force fields in Gromacs

g just the internal coordinates in the force field. Thanks in advance for any help and tips, Jernej Zidar -- 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 posti

[gmx-users] Use of non-standard CHARMM27 forcefield in Gromacs - how?

rt it into Gromacs? The files used in the Charmm simulations were: top_all27_lipid.rtf par_all27_lipid.rtf toppar_all27_lipid_cholesterol.str (the one containing the specific sphingomyelin bits) Thank you in advance for any tip or suggestion, Jernej Zidar -- gmx-users mailing listgmx-