Re: [gmx-users] Segmentation Fault (core dumped) in g_mmpbsapolar energy calculation

All the best!! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listin

Re: [gmx-users] Segmentation Fault (core dumped) in g_mmpbsa polar energy calculation

Sorry. My reply got posted into a new thread. Thanks Mark and Nikhil. @Mark reducing the no. of frame doesn't affect the results? @Nikhil I don't think it's APBS compatibility problem. I have installed Apbs 1.3 for my gromacs 4.5.7 as mentioned in the below tutorial. http://rashmikumari.githu

[gmx-users] Position restrain of structure

Dear all I have a structure file of cellulose nano fibril of 36 chain (each have 40 residue). I want to simulate it as a single compound. I try to run the simulation with OPLS-AA force field. After energy minimization when i run the equilibrium step then the fibril structure broken and all the chai

Re: [gmx-users] Analyse REMD

Thank you for your detailed steps! > 在 2016年5月31日，下午12:53，Christopher Neale 写道： > > Dear Ouyang: > > There is a script in the gromacs package (at least up to 5.1.2) called > demux.pl . You can use it to get more human friendly information out of your > REMD runs ( see http://www.gromac

[gmx-users] Segmentation Fault (core dumped) in g_mmpbsa

Thanks Mark and Nikhil. @Mark reducing the no. of frame doesn't affect the results? @Nikhil I don't think it's APBS compatibility problem. I have installed Apbs 1.3 for my gromacs 4.5.7 as mentioned in the below tutorial. http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html#so

Re: [gmx-users] Distance restraint and pull code

On 6/1/16 5:16 AM, HongTham wrote: Hi, Im now applying 4 pull codes to keep the Zn coordination. the script is like below. ; Pull code pull = umbrella pull-ngroups = 5 pull-ncoords = 4 pull-group1-name = ZN pull-group2-name = a_3862 pull-group3-name = a_1354 pull-group4-name = a_1390 pull-group

Re: [gmx-users] How to get an infinite DNA topology

On 6/1/16 11:40 AM, eli...@mail.ustc.edu.cn wrote: Hello everyone, I am working on a MD simulation using AMBER99 force field with gromacs in a system including a very long A-type DNA fragment. My plan is to build a cell containing exact 11 DNA base bair (which is a circle of A-type DNA), and wi

Re: [gmx-users] Clarity on TI free energy terms

On Wed, 1 Jun 2016 16:15:31 + "Nash, Anthony" wrote: > In the mean while, do you know of any tutorials (besides the methane > in water FE tutorial) regarding TI for amino acid substitution? I am not aware of one. You could try http://www.alchemistry.org/ > And by “q_off” and “vdw_on/off”

Re: [gmx-users] Clarity on TI free energy terms

In the mean while, do you know of any tutorials (besides the methane in water FE tutorial) regarding TI for amino acid substitution? And by “q_off” and “vdw_on/off”, I assume you are referring to the ‘value’ of the couple-lambda0: parameter? Thanks Anthony Dr Anthony Nash Department of Chemistry

Re: [gmx-users] Clarity on TI free energy terms

Thanks for all of this material. I’ll take some time and digest what you’ve said. No doubt I’ll have a few more questions tomorrow ;-) Thanks Anthony On 01/06/2016 16:38, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Hannes Loeffler" wrote: >On Wed, 1 Jun 2016 15:00:51 +00

[gmx-users] How to get an infinite DNA topology

Hello everyone, I am working on a MD simulation using AMBER99 force field with gromacs in a system including a very long A-type DNA fragment. My plan is to build a cell containing exact 11 DNA base bair (which is a circle of A-type DNA), and with periodic boundary conditions to get an infinite D

Re: [gmx-users] Clarity on TI free energy terms

On Wed, 1 Jun 2016 15:00:51 + "Nash, Anthony" wrote: > > This also assumes that > >you have vanishing atoms only. If you have appearing atoms only you > >would obviously have to revers the order, and when you have both you > >will have to run with two mdp/tpr setups. > > > With aspartic a

Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

> Il giorno 01 giu 2016, alle ore 11:18, Mark Abraham > ha scritto: > > Hi, > > Googling around, I see that some places recommend things such as > > export PATH=/Developer/NVIDIA/CUDA-6.0/bin:$PATH > export DYLD_LIBRARY_PATH=/Developer/NVIDIA/CUDA-6.0/lib:$DYLD_LIBRARY_PATH > > > Does that

[gmx-users] MoS2 OPLS-AA Parameterization

Dear GROMACS Users, I'm trying to modify the OPLS-AA force field parameters for Mo and S atoms to simulate monolayer MoS2. I'm following the general procedure suggested here: http://chembytes.wikidot.com/grocnt

Re: [gmx-users] Clarity on TI free energy terms

Dear Hannes, please see my comment below.. On 01/06/2016 14:45, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Hannes Loeffler" wrote: >On Wed, 1 Jun 2016 12:06:20 + >"Nash, Anthony" wrote: > >> vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 >> 0.40 0.4

Re: [gmx-users] Clarity on TI free energy terms

On Wed, 1 Jun 2016 12:06:20 + "Nash, Anthony" wrote: > vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 > 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 > mass_lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 > 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 >

Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1

Hi Mark, I know, but at that moment I wasn't working in the same room as the CPU and I wanted to be sure on what I had to try next. I tried the cmake command and got the same message. I used grep -R -I "CUDA_NVCC_FLAGS" and grep -R -I "CMAKE_CXX_FLAGS" to find what files I could try to add "-D_FORC

Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1

Hi Mark, I know, but at that moment I wasn't working in the same room as the CPU and I wanted to be sure on what I had to try next. I tried the cmake command and got the same message. I used grep -R -I "CUDA_NVCC_FLAGS" and grep -R -I "CMAKE_CXX_FLAGS" to find what files I could try to add "-D_FORC

Re: [gmx-users] Clarity on TI free energy terms

Hi Hannes, Thanks for the reply. At the moment for a change in single amino acid in a triplet (a pair of triplets, showing forward and reverse change) I am settling with: vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95

Re: [gmx-users] Clarity on TI free energy terms

Set the vector to all-zeroes (or ones). On Wed, 1 Jun 2016 09:47:59 + "Nash, Anthony" wrote: > Hi Hannes, > > > Many thanks for the reply. With regards to your final comment I > understand conserving mass in theory, but I am a little confused > regarding, "keep the mass-lambdas at one en

Re: [gmx-users] Clarity on TI free energy terms

Hi Hannes, Many thanks for the reply. With regards to your final comment I understand conserving mass in theory, but I am a little confused regarding, "keep the mass-lambdas at one end-point as they can interact badly with constraints". I am testing pmx on a two-molecule one-system I.e., G-D2K-G

Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

Hi, Googling around, I see that some places recommend things such as export PATH=/Developer/NVIDIA/CUDA-6.0/bin:$PATH export DYLD_LIBRARY_PATH=/Developer/NVIDIA/CUDA-6.0/lib:$DYLD_LIBRARY_PATH Does that seem adaptable to your setup as a possible fix for getting dynamic linking to work? Mark O

Re: [gmx-users] Distance restraint and pull code

Hi, Im now applying 4 pull codes to keep the Zn coordination. the script is like below. ; Pull code pull = umbrella pull-ngroups = 5 pull-ncoords = 4 pull-group1-name = ZN pull-group2-name = a_3862 pull-group3-name = a_1354 pull-group4-name = a_1390 pull-group5-name = a_1721 pull-geometry = distanc

[gmx-users] Error while generating ions.tpr file

Dear Mark, Thanks for your suggestion! Kamakshi Sikka -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit h

Re: [gmx-users] Clarity on TI free energy terms

On Wed, 1 Jun 2016 07:54:56 + "Nash, Anthony" wrote: > In the tutorial, charges are off in the topology and the electrostatic > coupling to lambda remains 0 throughout the 20 windows. I assume > setting col_lambdas=0 0 0 Š was for that very reason I.e., the > charges were off? Could the charg

Re: [gmx-users] Segmentation Fault (core dumped) in g_mmpbsapolar energy calculation

Please see the previous mailing list,this problem normally occurs incompatible APBS and g_mmpbsa check your installation carefully -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http:

Re: [gmx-users] Segmentation Fault (core dumped) in g_mmpbsa polar energy calculation

Hi, You can probe for memory issues by running subsets of your original calculation, e.g. fewer trajectory frames (or however g_mmpbsa works). Mark On Wed, Jun 1, 2016 at 10:16 AM Pavithra wrote: > Dear users, > > I have installed g_mmpbsa package for MMPBSA calculation in gromacs. > > When I

[gmx-users] Segmentation Fault (core dumped) in g_mmpbsa polar energy calculation

Dear users, I have installed g_mmpbsa package for MMPBSA calculation in gromacs. When I execute MM calculations, there is no problem. But when I execute polar calculations, I get Segmentation Fault (core dumped) error. I tried the tutorial files, and getting the same error in polar calculations

[gmx-users] Clarity on TI free energy terms

Dear all, I¹m trying to understand the finesse behind the TI free energy in gromacs, before taking it anywhere near a real production run, by running through the FE methane in solvent tutorial and the thermodynamic cycles of small peptides in the PMX paper. I roughly-understand a fair chunk, howev

[gmx-users] Time of NPT and NVT running

Hi everybody,   I am simulating a peptide in a box of water with differentconcentration of water. The system has about 14000 molecules of water. The runningof NVT and NPT simulation last about 1 hour with the time step of 100 ps. When therunning is completed I check the diagram of temperature