[gmx-users] Error using pdb2gmx tool

hi, I was simulating A cadherin molecule (PDB ID: 4APX). I removed all the water molecule from molecule then ran the following command. pdb2gmx -f 4APX.pdb -water tip3p then I chose force field : CHARMM27 (with CMAP) after that it should create 3 types of files (.gro, .itp, .top) but it is not g

Re: [gmx-users] CUDA5.5 and ICC 14

Thanks! On 8/20/2014 8:03 PM, Mark Abraham wrote: Hi, Per Nvidia's docs and that error, CUDA 5.5 is only supported with that icc version. In practice, I understand that other icc versions work fine with GROMACS, but you would need to go and comment out that #error message. Alternatively, CUDA 6

Re: [gmx-users] Install errors

Thanks! 2014-08-20 14:05 GMT+02:00 Mark Abraham : > Hi, > > You should be using a supported host compiler for your version of CUDA > (check its docs, probably gcc 4.7 or 4.8, for example), rather than clang. > > Mark > > > On Wed, Aug 20, 2014 at 9:59 AM, Valentina Loconte < > valentina.loco...@

Re: [gmx-users] Error using pdb2gmx tool

On 8/21/14, 5:24 AM, ankit agrawal wrote: hi, I was simulating A cadherin molecule (PDB ID: 4APX). I removed all the water molecule from molecule then ran the following command. pdb2gmx -f 4APX.pdb -water tip3p then I chose force field : CHARMM27 (with CMAP) after that it should create 3 type

Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues

Hi Tom, Thanks, I will look into it. I know AMBER has the ZAFF forcefield, and I have done the simulation in AMBER, but I wanted to know if GROMOS forcefields have this capability. I will have a play and see what I can do, most likely I will do a small QM/MM run and use this to parameterise th

Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues

Hi, QM parameterisation is how people tend to have done it for things like copper-bound proteins with GROMOS. I have been recently simulating one of these copper-bound proteins using a GROMOS force field (and indeed an AMBER force field too). I can send you a couple of papers regarding the GROM

[gmx-users] How invoke hamiltonian replica exchange in 4.6.5

Dear gmx users: I got a problem that I could not invoke hamiltonian replica exchange in version 4.6.5. I've different lambda value for each replica ( free_energy = yes; init-lambda = 0.X ) however I got error "the properties of the 4 systems arre all the same..." I've tried the metho

Re: [gmx-users] Several questions about log file.

On Thu, Aug 21, 2014 at 7:57 AM, Theodore Si wrote: > Hi, > > 1. Does "force" in the R E A L C Y C L E A N D T I M E A C C O U N > T I N G table mean the time spent on short-range force calculation? > and bonded interactions. > 2. Does "Comm. coord" mean the communication of atom posit

Re: [gmx-users] REMD tutorial

On Thu, Aug 21, 2014 at 8:01 AM, shahab shariati wrote: > Dear Mark > > Before, in following address you said: Google knows about two GROMACS REMD > tutorials. > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-January/086563.html > > Unfortunately, I could not find tutorials

Re: [gmx-users] How invoke hamiltonian replica exchange in 4.6.5

Are your temperatures the same in each replica? Mark On Thu, Aug 21, 2014 at 4:08 PM, jia jia wrote: > Dear gmx users: > I got a problem that I could not invoke hamiltonian replica exchange in > version 4.6.5. I've different lambda value for each replica ( > free_energy = yes; init-lambda

[gmx-users] regarding MSD

Hello all I have read few papers that determine transition temperature from the plot of average MSD versus temperature. My question is: At a particular temperature, we get a linear curve for MSD versus time, is it reasonable to calculate average MSD over all such time points? Is this the average t

Re: [gmx-users] Extending simulation problem.

Well in my *log file nothing about state or *cpi files is mentioned. Acutally I have a question regarding state.cpi files. Does it contain names of *gro, *trr, etc. files if they are not standard? The thing is, that output files from my first 5ns simulation are not standard. Now, I perform these ca

Re: [gmx-users] Extending simulation problem.

On Thu, Aug 21, 2014 at 6:28 PM, Dawid das wrote: > Well in my *log file nothing about state or *cpi files is mentioned. > Sounds like perhaps your combination of circumstances (-append, no old output files provided for appending, maybe not even a checkpoint file provided) is leading to mdrun si

Re: [gmx-users] [gmx-developers] About dynamics loading balance

Hi, please don't use gmx-developers for user questions. Feel free to use it if you want to fix the problem, and have questions about implementation details. Please provide more details: How large is your system? How much memory does a node have? On how many nodes do you try to run? How many mpi-r

Re: [gmx-users] Numerical Stability of Gromacs Implementation

Sorry for asking this. Is it possible for me to get some references about the claims of instability of gromacs simulations, and their debunk? >From the few papers that I read, I guess algorithms of molecular dynamics do not treat all observables equally well. Some old papers say that the velocity

Re: [gmx-users] [gmx-developers] About dynamics loading balance

Hi, On Thu, Aug 21, 2014 at 1:56 PM, Yunlong Liu wrote: > Hi Roland, > > The problem I am posting is caused by trivial errors (like not enough > memory) and I think it should be a real bug inside the gromacs-GPU support > code. > It is unlikely a trivial error because otherwise someone else wo

Re: [gmx-users] [gmx-developers] About dynamics loading balance

Hi Roland, I just compiled the latest gromacs-5.0 version released on Jun 29th. I will recompile it as you suggested by using those Flags. It seems like the high loading imbalance doesn't affect the performance as well, which is weird. Thank you. Yunlong On 8/21/14, 2:13 PM, Roland Schulz wr

[gmx-users] GROMACS version 5.0 incompatible with my hardware - help req

Dear Users I initially installed GROMACS 5.0 in my office computer and tried running a few sample tutorials over there. It was showing a "illegal instruction : core dumped "error. On searching the archived files in the user group I found that the version of GROMACS installed in my computer is not

Re: [gmx-users] GROMACS version 5.0 incompatible with my hardware - help req

where did you get gromacs? how did you install it? (like you compile it yourself, or you get the package with apt-get?) On Thu, Aug 21, 2014 at 3:11 PM, Agnivo Gosai wrote: > Dear Users > > I initially installed GROMACS 5.0 in my office computer and tried running a > few sample tutorials over

Re: [gmx-users] GROMACS version 5.0 incompatible with my hardware - help req

or.. you get it from some rpm/deb binary file that is for another kind of cpu? On Thu, Aug 21, 2014 at 3:44 PM, Johnny Lu wrote: > where did you get gromacs? > how did you install it? (like you compile it yourself, or you get the > package with apt-get?) > > > > On Thu, Aug 21, 2014 at 3:11 PM,

Re: [gmx-users] GROMACS version 5.0 incompatible with my hardware - help req

On 8/21/14, 3:11 PM, Agnivo Gosai wrote: Dear Users I initially installed GROMACS 5.0 in my office computer and tried running a few sample tutorials over there. It was showing a "illegal instruction : core dumped "error. On searching the archived files in the user group I found that the versi

[gmx-users] pressure after NPT

dear gromacs users, I am simulating Carbon nanotubes in water. I did the NPT simulation with a reference pressure of 1 bar. When I do an NPT simulation for about 100 ps, the system shows an average pressure of 1.4 bar. So i thought a longer NPT simulation would give me a better average pressure. B

Re: [gmx-users] pressure after NPT

On 8/21/14, 4:22 PM, ibrahim khalil wrote: dear gromacs users, I am simulating Carbon nanotubes in water. I did the NPT simulation with a reference pressure of 1 bar. When I do an NPT simulation for about 100 ps, the system shows an average pressure of 1.4 bar. So i thought a longer NPT simula

[gmx-users] Interteting flooding results

Dear users, could anyone give me some general guidelines or links to help me interpret the essential dynamics/flooding output xvg file from a flooding simulation? I followed Spiwok's tutorial (http://web.vscht.cz/~spiwokv/mtdec/index.html) and Langer's paper (http://onlinelibrary.wiley.com/doi

Re: [gmx-users] Numerical Stability of Gromacs Implementation

On Thu, Aug 21, 2014 at 7:59 PM, Johnny Lu wrote: > Sorry for asking this. Is it possible for me to get some references about > the claims of instability of gromacs simulations, and their debunk? > Not really. You can find a paper from some of the Desmond authors that correctly observes some iss

[gmx-users] Job Submission script for Multiple nodes GPUs calculation

Good afternoon, I am trying to use multiple nodes to do GPU simulation, each node has two GPUs and 12 CPUs mounted. Is there any submission script for doing that? For single node I used: mpiexec -np 2 mdrun_mpi -s run.tpr -cpi state.cpt -cpo state.cpt -noappend -gpu_id 01 -nb gpu -ntomp 6 For 2

Re: [gmx-users] too many lincs warnings

Thanks.. On Aug 20, 2014 1:29 PM, "Meenakshi Rajput" wrote: > hello users > I had done energy minimisation of protein-ligand complex and i got > negative potential. Also the ligand was at right place after EM run but > when I tried the positional restrained run, too many lincs warnings came > and

Re: [gmx-users] Job Submission script for Multiple nodes GPUs calculation

Hi, On 22 Aug 2014, at 01:38, Xingcheng Lin wrote: > Good afternoon, > > I am trying to use multiple nodes to do GPU simulation, each node has two > GPUs and 12 CPUs mounted. Is there any submission script for doing that? > > For single node I used: > > mpiexec -np 2 mdrun_mpi -s run.tpr -cpi

Re: [gmx-users] Interteting flooding results

Hi, On 21 Aug 2014, at 23:27, Ricardo O. S. Soares wrote: > Dear users, > > could anyone give me some general guidelines or links to help me interpret > the essential dynamics/flooding output xvg file from a flooding simulation? That depends a bit on which Gromacs Version you are using. If y

Re: [gmx-users] regarding MSD

Hello I have posted the query earlier but havent got any reply and so reposting it again. I have read few papers that determine transition temperature from the plot of average MSD of hydrogen atoms of protein versus temperature. My question is: At a particular temperature, we get a linear curve f