Re: [gmx-users] REMD stall out

This was not actually the solution. Wanted to follow up in case someone else is experiencing this problem. We are reinstalling the openmp version. On Thu, Feb 20, 2020 at 3:10 PM Daniel Burns wrote: > Hi again, > > It seems including our openmp module was responsible for the issue the > whole

Re: [gmx-users] REMD stall out

Hi again, It seems including our openmp module was responsible for the issue the whole time. When I submit the job only loading pmix and gromacs, replica exchange proceeds. Thank you, Dan On Mon, Feb 17, 2020 at 9:09 AM Mark Abraham wrote: > Hi, > > That could be caused by configuration of

Re: [gmx-users] REMD stall out

Thanks Mark and Szilard, I forwarded Mark's suggestion to IT. I'll see what they have to say and then I'll try the simulation again and open an issue on redime. Thank you, Dan On Mon, Feb 17, 2020 at 9:09 AM Mark Abraham wrote: > Hi, > > That could be caused by configuration of the parallel

Re: [gmx-users] REMD stall out

Hi, That could be caused by configuration of the parallel file system or MPI on your cluster. If only one file descriptor is available per node to an MPI job, then your symptoms are explained. Some kinds of compute jobs follow such a model, so maybe someone optimized something for that. Mark On

Re: [gmx-users] REMD stall out

Hi Dan, What you describe in not an expected behaviro and it is something we should look into. What GROMACS version were you using? One thing that may help diagnosing the issue is: try to disable replica exchange and run -multidir that way. Does the simulation proceed? Can you please open an

Re: [gmx-users] REMD stall out

HI Szilard, I've deleted all my output but all the writing to the log and console stops around the step noting the domain decomposition (or other preliminary task). It is the same with or without Plumed - the TREMD with Gromacs only was the first thing to present this issue. I've discovered

Re: [gmx-users] REMD stall out

Hi, If I understand correctly your jobs stall, what is in the log output? What about the console? Does this happen without PLUMED? -- Szilárd On Tue, Feb 11, 2020 at 7:56 PM Daniel Burns wrote: > Hi, > > I continue to have trouble getting an REMD job to run. It never makes it > to the point

[gmx-users] REMD stall out

Hi, I continue to have trouble getting an REMD job to run. It never makes it to the point that it generates trajectory files but it never gives any error either. I have switched from a large TREMD with 72 replicas to the Plumed Hamiltonian method with only 6 replicas. Everything is now on one

[gmx-users] REMD

Hello gmx users, I am getting an error "load imbalance " in remd nvt equilibrium step. Can anyone help me regarding this issue? Thanks -- 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

Re: [gmx-users] REMD-error

Thank you for your email sir. On Wed, Sep 4, 2019 at 2:42 PM Mark Abraham wrote: > Hi, > > On Wed, 4 Sep 2019 at 10:47, Bratin Kumar Das <177cy500.bra...@nitk.edu.in > > > wrote: > > > Respected Mark Abraham, > > The command-line and the job > >

Re: [gmx-users] REMD-error

Hi, On Wed, 4 Sep 2019 at 10:47, Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Respected Mark Abraham, > The command-line and the job > submission script is given below > > #!/bin/bash > #SBATCH -n 130 # Number of cores > Per the docs, this is

Re: [gmx-users] REMD-error

Respected Mark Abraham, The command-line and the job submission script is given below #!/bin/bash #SBATCH -n 130 # Number of cores #SBATCH -N 5 # no of nodes #SBATCH -t 0-20:00:00 # Runtime in D-HH:MM #SBATCH -p cpu # Partition to submit to #SBATCH -o

Re: [gmx-users] REMD-error

Hi, We need to see your command line in order to have a chance of helping. Mark On Wed, 4 Sep 2019 at 05:46, Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Dear all, > I am running one REMD simulation with 65 replicas. I am using > 130 cores for the simulation. I am

[gmx-users] REMD-error

Dear all, I am running one REMD simulation with 65 replicas. I am using 130 cores for the simulation. I am getting the following error. Fatal error: Your choice of number of MPI ranks and amount of resources results in using 16 OpenMP threads per rank, which is most likely

Re: [gmx-users] REMD

Thanks for clarification. On Thu, Aug 1, 2019 at 7:43 PM Justin Lemkul wrote: > > > On 7/31/19 1:44 AM, Bratin Kumar Das wrote: > > Hi, > > I have some doubt regarding REMD simulation. > > 1. In the .mdp file of each replica is it necessary to keep the > > gen-temp constant? > > as

Re: [gmx-users] REMD

On 7/31/19 1:44 AM, Bratin Kumar Das wrote: Hi, I have some doubt regarding REMD simulation. 1. In the .mdp file of each replica is it necessary to keep the gen-temp constant? as example: 300 k is the lowest temp of REMD simulation. Is it necessary to keep the gen-temp=300 in each

[gmx-users] REMD

Hi, I have some doubt regarding REMD simulation. 1. In the .mdp file of each replica is it necessary to keep the gen-temp constant? as example: 300 k is the lowest temp of REMD simulation. Is it necessary to keep the gen-temp=300 in each replica. 2. Is it necessary to provide -replex

Re: [gmx-users] remd error

Thank you On Mon 29 Jul, 2019, 6:45 PM Justin Lemkul, wrote: > > > On 7/29/19 7:55 AM, Bratin Kumar Das wrote: > > Hi Szilard, > > Thank you for your reply. I rectified as you said. For > trial > > purpose i took 8 nodes or 16 nodes... (-np 8) to text whether it is > running > >

Re: [gmx-users] remd error

On 7/29/19 7:55 AM, Bratin Kumar Das wrote: Hi Szilard, Thank you for your reply. I rectified as you said. For trial purpose i took 8 nodes or 16 nodes... (-np 8) to text whether it is running or not. I gave the following command to run remd *mpirun -np 8 gmx_mpi_d mdrun -v

Re: [gmx-users] remd error

Hi Szilard, Thank you for your reply. I rectified as you said. For trial purpose i took 8 nodes or 16 nodes... (-np 8) to text whether it is running or not. I gave the following command to run remd *mpirun -np 8 gmx_mpi_d mdrun -v -multi 8 -replex 1000 -deffnm remd* After giving the

Re: [gmx-users] remd error

This is an MPI / job scheduler error: you are requesting 2 nodes with 20 processes per node (=40 total), but starting 80 ranks. -- Szilárd On Thu, Jul 18, 2019 at 8:33 AM Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > > Hi, >I am running remd simulation in gromacs-2016.5. After

[gmx-users] remd error

Hi, I am running remd simulation in gromacs-2016.5. After generating the multiple .tpr file in each directory by the following command *for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro -p topol.top -o remd$i.tpr -maxwarn 1; cd ..; done* I run *mpirun -np 80 gmx_mpi mdrun -s

Re: [gmx-users] REMD - subsystems not compatible

Thanks Mark for reminding me about the existence of the log files. Problem solved, the difference is clearly indicated (number of atoms, my stupid mistake. Cheers /Per > 24 apr. 2019 kl. 16:51 skrev Mark Abraham : > > Hi, > > Generally the REMD code has written some analysis to the log

[gmx-users] REMD - subsystems not compatible

Hi gmx-users, I am trying to start a replica exchange simulation of a model peptide in water, but can’t get it to run properly. I have limited experience with REMD, so I thought I’d ask here for all the rookie mistakes it is possible to do. I have also seen the earlier discussions about the

Re: [gmx-users] REMD Plots

Hi Joel, Thank you very much. On Wed, Jan 9, 2019 at 3:27 PM Joel Awuah wrote: > Hi Shan, > I am not quite sure if you want to generate an REMD simulation mobility in > temperature space for the 30 replicas. If that be the case, then you can > use the data in the replica_temperature.xvg file

Re: [gmx-users] REMD Plots

Hi Shan, I am not quite sure if you want to generate an REMD simulation mobility in temperature space for the 30 replicas. If that be the case, then you can use the data in the replica_temperature.xvg file to plot replica index vs REMD steps. The 1st column in the file corresponds to the REMD

[gmx-users] REMD Plots

Dear Gromacs users, How do we plot a graph for temperature vs swap step number using a REMD simulation with 30 systems. I already generated the replica_temp.xvg and replica_index.xvg files using demux.pl script. Thank you. Best Regards Shan Jayasinghe -- Gromacs Users mailing list * Please

[gmx-users] REMD Simulation for a system at different Concentration

Dear all, I am planning to do REMD for a system containing Protein, Urea, Osmolyte and water, I want to generate the temperature replica. So the REMD temperature generator asks for number of water molecules only, but here in my case there are something more in the system, So is it fine that I

Re: [gmx-users] REMD Showing Zero Exchange Probability

Sorry for the delay..Thank you Mark.. On Sat, Jul 21, 2018 at 2:09 AM, Mark Abraham wrote: > Hi, > > You can't arbitrarily choose both the temperature range and number of > replicas and get non-zero exchange probability. See > https://pubs.acs.org/action/showCitFormats?doi=10.1021%2Fct800016r.

Re: [gmx-users] REMD Showing Zero Exchange Probability

Hi, You can't arbitrarily choose both the temperature range and number of replicas and get non-zero exchange probability. See https://pubs.acs.org/action/showCitFormats?doi=10.1021%2Fct800016r. For a given average exchange probability, choose a range and thus the number of replicas, or the number

Re: [gmx-users] REMD Showing Zero Exchange Probability

Ligesh > > Lichu > > Sent: Friday, July 20, 2018 4:39 AM > > To: gmx-us...@gromacs.org > > Subject: [gmx-users] REMD Showing Zero Exchange Probability > > > > Dear all, > > I have performed REMD for a system containing Protein, Reline, Urea > and &

Re: [gmx-users] REMD Showing Zero Exchange Probability

t: Friday, July 20, 2018 4:39 AM > To: gmx-us...@gromacs.org > Subject: [gmx-users] REMD Showing Zero Exchange Probability > > Dear all, > I have performed REMD for a system containing Protein, Reline, Urea and > Water in the temperature range 290 to 450 K consist of 16 replic

Re: [gmx-users] REMD Showing Zero Exchange Probability

...@maillist.sys.kth.se on behalf of Ligesh Lichu Sent: Friday, July 20, 2018 4:39 AM To: gmx-us...@gromacs.org Subject: [gmx-users] REMD Showing Zero Exchange Probability Dear all, I have performed REMD for a system containing Protein, Reline, Urea and Water in the temperature range 290 to 450 K

[gmx-users] REMD Showing Zero Exchange Probability

Dear all, I have performed REMD for a system containing Protein, Reline, Urea and Water in the temperature range 290 to 450 K consist of 16 replicas out of 47 replicas generated by REMD temperature generator. But after the MD simulation the exchange probability is zero. I have used position

[gmx-users] REMD

Hello GROMACS users, As far as I understand, increasing the number of random exchanges to a large number (mdrun suggests N^3 where N is the number of replicas) moves a REMD simulation from a neighbor exchange procedure to a Gibbs exchange procedure. Can anyone provide some practical advice or

[gmx-users] REMD

Hello Gromacs Users, I am interested in calculating the equilibrium distribution of molecular structures at the vacuum-liquid interface of several different low vapor pressure liquids. All of these liquids are very viscous at or near room-temperature and I suspect that conformational barriers may

Re: [gmx-users] REMD temperature_space

Hi, Unfortunately nobody has implemented demux for the energy files. You could consider contributing a modification of demux.pl :-) Mark On Fri, May 4, 2018 at 8:42 AM Sundari wrote: > Hello Guys, > > Kindly suggest me something about my doubt. > > On Thu, May 3, 2018 at

Re: [gmx-users] REMD temperature_space

Hello Guys, Kindly suggest me something about my doubt. On Thu, May 3, 2018 at 5:19 PM, Sundari wrote: > Hello, > > I got the continuous trajectories by using demux. But now I am confused in > getting potential energy distribution of a single replica (similarly time >

Re: [gmx-users] REMD temperature_space

Hello, I got the continuous trajectories by using demux. But now I am confused in getting potential energy distribution of a single replica (similarly time evolution of a replica (say replica_1) in temperature space). I used edr file of original production data files, but I am not getting what I

Re: [gmx-users] REMD temperature_space

Hi, It sounds like you just want to use the original data, which you had before you ran the demux script. Mark On Thu, May 3, 2018 at 1:28 PM Sundari wrote: > Dear gromacs users, > > can anyone please suggest me that how we get the time evolution of a > replica (say

[gmx-users] REMD temperature_space

Dear gromacs users, can anyone please suggest me that how we get the time evolution of a replica (say replica_1) in temperature space and time courses of potential energy of each replica( one way is md.edr file??) As according to GROMACS tutorial, I used demux.pl script and got two files

Re: [gmx-users] REMD Simulation

Hi, On Mon, Apr 16, 2018 at 10:21 AM ISHRAT JAHAN wrote: > Dear all, > I am trying to do REMD simulation in different cosolvents. I have generated > temperatures using temperature genrating tools but it gives different > number of temperatures in different solvents with

[gmx-users] REMD Simulation

Dear all, I am trying to do REMD simulation in different cosolvents. I have generated temperatures using temperature genrating tools but it gives different number of temperatures in different solvents with exchange probability of 0.25. Is it fair to do remd with different replicas? In what way it

Re: [gmx-users] REMD DLB bug

Hi, The fix will be released in an upcoming 2016.5 patch release. (which you can see in the redmine issue page "Target version" field BTW). Cheers, -- Szilárd On Mon, Feb 12, 2018 at 2:49 PM, Akshay wrote: > Hello All, > > I was running REMD simulations on Gromacs

[gmx-users] REMD DLB bug

Hello All, I was running REMD simulations on Gromacs 2016.1 when my simulation crashed with the error Assertion failed: Condition: comm->cycl_n[ddCyclStep] > 0 When we turned on DLB, we should have measured cycles I saw that there was a bug #2298 reported about this recently at

Re: [gmx-users] REMD implicit solvent

Hi, I should run it by using mdrun_mpi? best Urszula > Hello, > > From my experience, the domain decomposition is not compatible with > implicit solvent, you have to switch > to particle decomposition for the simulations. > > > All the best, > Qinghua > > On 01/05/2018 12:40 PM, Urszula

Re: [gmx-users] REMD implicit solvent

Hello, From my experience, the domain decomposition is not compatible with implicit solvent, you have to switch to particle decomposition for the simulations. All the best, Qinghua On 01/05/2018 12:40 PM, Urszula Uciechowska wrote: Hi, I just run a normal single-replica. Now the error

Re: [gmx-users] REMD implicit solvent

Hi, I just run a normal single-replica. Now the error that I have is: Program mdrun_mpi, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS

Re: [gmx-users] REMD implicit solvent

Hi, Did you try to debug your setup by running a normal single-replica simulation first? Mark On Fri, Jan 5, 2018 at 12:12 PM Urszula Uciechowska < urszula.uciechow...@biotech.ug.edu.pl> wrote: > > > Dear gromacs users, > > I am trying to run REMD simulations using 4.5.5 version (implicit >

[gmx-users] REMD implicit solvent

Dear gromacs users, I am trying to run REMD simulations using 4.5.5 version (implicit solvent). The MD procedure: pdb2gmx -f prot.pdb -o prot.gro -q prot.pdb -ignh -ss. The input for minimization step: ; Run control parameters integrator = cg nsteps = 800 vdwtype

Re: [gmx-users] REMD analysis of trajectories

<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abra...@gmail.com> Sent: Thursday, June 01, 2017 10:53 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] REMD analysis of trajectories Hi, What did you learn from the first sentence of the lin

Re: [gmx-users] REMD analysis of trajectories

Hi, What did you learn from the first sentence of the link I gave you? Mark On Thu, Jun 1, 2017 at 3:20 PM YanhuaOuyang <15901283...@163.com> wrote: > Do you mean that the original trajectories REMD generated are belong to > "one trajectory per temperature" (i.e. the md2.xtc is a trajectory

Re: [gmx-users] REMD analysis of trajectories

Do you mean that the original trajectories REMD generated are belong to "one trajectory per temperature" (i.e. the md2.xtc is a trajectory at 298K)? Ouyang At 2017-06-01 21:00:52, "Mark Abraham" wrote: >Hi, > >That's what you already have. See

Re: [gmx-users] REMD analysis of trajectories

Hi, That's what you already have. See http://www.gromacs.org/Documentation/How-tos/REMD#Post-Processing Mark On Thu, Jun 1, 2017 at 5:37 AM YanhuaOuyang <15901283...@163.com> wrote: > Hi, >I have run a 100ns-REMD of protein, which has 20 replicas (i.e. > remd1.xtc, remd2.xtc, ...,

[gmx-users] REMD analysis of trajectories

Hi, I have run a 100ns-REMD of protein, which has 20 replicas (i.e. remd1.xtc, remd2.xtc, ..., remd20.xtc). I want to analyze a trajectory at specific temperature such as a trajectory at experiment temperature 298K rather than analyzing the continuous trajectory. I have known GROMACS

[gmx-users] REMD analysis

Dear all, I have performed an REMD simulation for protein drug system (8350 + 32500 sol) using gromacs-4.4.5 package. But I could not understand how to do analysis of REMD. I have used 10 set of replicas (298 K to 308.31K with r=1.0038, the common ratio of the geometric progression) for REMD

Re: [gmx-users] REMD ensemble of states

gmail.com> Sent: Monday, November 14, 2016 1:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] REMD ensemble of states Hi, The ensemble at each temperature is intrinsically discontinuous. You can't make it look continuous. What are you trying to do? Mark On Mon, 14 Nov 2016 05:26 Abramyan,

Re: [gmx-users] REMD ensemble of states

Subject: Re: [gmx-users] REMD ensemble of states Yes On Tue, 8 Nov 2016 18:43 Abramyan, Tigran <tig...@email.unc.edu> wrote: > Hi Mark, > > Thanks a lot for your prompt response. So demux.pl creates continuous > trajectories, *_trajout.xtc, but the ensemble of states (lowes

Re: [gmx-users] REMD ensemble of states

maillist.sys.kth.se> on behalf of Mark > Abraham <mark.j.abra...@gmail.com> > Sent: Tuesday, November 8, 2016 5:53 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] REMD ensemble of states > > Hi, > > Mdrun wrote that. You made the trajectories conti

Re: [gmx-users] REMD ensemble of states

.org Subject: Re: [gmx-users] REMD ensemble of states Hi, Mdrun wrote that. You made the trajectories contiguous with the demux. Mark On Tue, 8 Nov 2016 04:55 Abramyan, Tigran <tig...@email.unc.edu> wrote: > Hi, > > > I conducted REMD, and extracted the trajectorie

Re: [gmx-users] REMD ensemble of states

Hi, Mdrun wrote that. You made the trajectories contiguous with the demux. Mark On Tue, 8 Nov 2016 04:55 Abramyan, Tigran wrote: > Hi, > > > I conducted REMD, and extracted the trajectories via > trjcat -f *.trr -demux replica_index.xvg > And now I was wondering which

[gmx-users] REMD ensemble of states

Hi, I conducted REMD, and extracted the trajectories via trjcat -f *.trr -demux replica_index.xvg And now I was wondering which *.xtc file is the ensemble of states at the baseline replica (lowest temperature replica). Intuitively my guess is that the numbers in the names of *_trajout.xtc

Re: [gmx-users] REMD - replicas sampling in temperatures beyond the assigned range

Hi, Best practice is to read and learn others practice from publications that are similar to what you want to do, rather than making ad-hoc changes. In this case, the GROMACS defaults are pretty close to the de facto standard, and supported by analysis work done by other members of the community.

Re: [gmx-users] REMD - replicas sampling in temperatures beyond the assigned range

Dear Justin, Thanks a lot for pointing out the issues. I now understand why there were such high oscillations. Could you please also tell me if there are any ideal values for pme_order and fourier spacing with respect to the cut offs' value of 1.4. Does the following Note imply I can raise the

Re: [gmx-users] REMD - replicas sampling in temperatures beyond the assigned range

On 6/30/16 9:16 AM, NISHA Prakash wrote: Dear Justin, Thank you for your reply. It is a protein carbohydrate system. Including the solvent, the number of atoms is 43499. I have minimized the system for 200 ps followed by NPT and NVT simulations for 200 ps respectively Given that your

Re: [gmx-users] REMD - replicas sampling in temperatures beyond the assigned range

Dear Justin, Thank you for your reply. It is a protein carbohydrate system. Including the solvent, the number of atoms is 43499. I have minimized the system for 200 ps followed by NPT and NVT simulations for 200 ps respectively Below is the .mdp file. ; VARIOUS PREPROCESSING OPTIONS title

Re: [gmx-users] REMD - replicas sampling in temperatures beyond the assigned range

On 6/30/16 8:46 AM, NISHA Prakash wrote: Dear all, I have conducted a 10ns REMD simulation for a protein ligand complex with the temperature range - 270 to 350 K, however the temperature distribution plot of the replicas show that the sampling has occurred at higher temperatures as well that

[gmx-users] REMD - replicas sampling in temperatures beyond the assigned range

Dear all, I have conducted a 10ns REMD simulation for a protein ligand complex with the temperature range - 270 to 350 K, however the temperature distribution plot of the replicas show that the sampling has occurred at higher temperatures as well that is beyond 350K - Below is an excerpt from the

Re: [gmx-users] REMD error

Hi, If you've configured with GMX_MPI, then the resulting GROMACS binary is called gmx_mpi, so mpirun -np X gmx_mpi mdrun -multi ... Mark On Fri, May 13, 2016 at 10:09 AM YanhuaOuyang <15901283...@163.com> wrote: > Hi, > I have installed the openmpi 1.10, and I can run mpirun. When I installed

Re: [gmx-users] REMD error

Hi, I have installed the openmpi 1.10, and I can run mpirun. When I installed grimaces 5.1, I configured -DGMX_MPI=on. And the error still happens . > 在 2016年5月13日，下午3:59，Mark Abraham 写道： > > Hi, > > Yes. Exactly as the error message says, you need to compile GROMACS

Re: [gmx-users] REMD error

Hi, Yes. Exactly as the error message says, you need to compile GROMACS differently, with real MPI support. See http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-features.html#running-multi-simulations Mark On Fri, May 13, 2016 at 9:47 AM YanhuaOuyang <15901283...@163.com> wrote:

[gmx-users] REMD error

Hi, I am running a REMD of a protein, when I submit "gmx mdrun -s md_0_${i}.tpr -multi 46 -replex 1000 -reseed -1", it fails as the below Fatal error: mdrun -multi or -multidir are not supported with the thread-MPI library. Please compile GROMACS with a proper external MPI library. I have

Re: [gmx-users] REMD on more than one node

Hi, You'll need to choose a replica setup that naturally fits on your available hardware. Number of nodes * number of cores per node must equal number of replicas * number of cores per replica. See also

[gmx-users] REMD on more than one node

Hi, I am running a REMD with grimacs 5.0, I have 46 replica, 4 nodes, 16 cores per node. how can I use my compute resource and what’s the command of “gmx mdrun”? the command is below, I am not sure weather it is right mpirun -np 4 -npme gmx mdrun -s md_01.tpr -multi 46 -replex 500 -reseed -1.

Re: [gmx-users] REMD--how to determine the temperature distribution

s.org_gmx-users-boun...@maillist.sys.kth.se < >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of >> YanhuaOuyang <15901283...@163.com> >>> Sent: 25 April 2016 10:36 >>> To: gmx-us...@gromacs.org >>> Subject: [gmx-users] REMD--how

Re: [gmx-users] REMD--how to determine the temperature distribution

sers-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > YanhuaOuyang <15901283...@163.com> > > Sent: 25 April 2016 10:36 > > To: gmx-us...@gromacs.org > > Subject: [gmx-users] REMD--how to determine the temperature distr

Re: [gmx-users] REMD--how to determine the temperature distribution

com> > Sent: 25 April 2016 10:36 > To: gmx-us...@gromacs.org > Subject: [gmx-users] REMD--how to determine the temperature distribution > > Dear all, >I am going to run a REMD of a protein(explicit solvent) in NVT > ensemble with gromacs, but I have trouble in determi

Re: [gmx-users] REMD--how to determine the temperature distribution

gmx-users-boun...@maillist.sys.kth.se> on behalf of YanhuaOuyang <15901283...@163.com> Sent: 25 April 2016 10:36 To: gmx-us...@gromacs.org Subject: [gmx-users] REMD--how to determine the temperature distribution Dear all, I am going to run a REMD of a protein(explicit solvent) in

[gmx-users] REMD--how to determine the temperature distribution

Dear all, I am going to run a REMD of a protein(explicit solvent) in NVT ensemble with gromacs, but I have trouble in determining a optimum temperature distribution.Can anybody know the ways to determine the temperature? -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] REMD of IDPs

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of João Henriques <joao.henriques.32...@gmail.com> Sent: Friday, April 08, 2016 8:24 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] REMD of IDPs One

Re: [gmx-users] REMD of IDPs

; > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of João > Henriques <joao.henriques.32...@gmail.com> > Sent: Friday, April 08, 2016 3:51 AM > To: Dis

Re: [gmx-users] REMD of IDPs

rs-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of João Henriques <joao.henriques.32...@gmail.com> Sent: Friday, April 08, 2016 3:51 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] REMD of IDPs ​Dear Yanhua, To m

Re: [gmx-users] REMD of IDPs

​Dear Yanhua, To my knowledge (prior to gromacs 5.X at least), there​ are no gromacs tools able to turn a sequence into a PDB. The user must take care of that pre-processing on his/her own. I work with IDPs quite a lot, so what I can tell you is what I usually do. I take my fasta sequence and use

[gmx-users] REMD of IDPs

Hi, I have a sequence of an intrinsically disordered protein, I have no idea how to start my REMD with gromacs. e.g. how to convert my sequence into a pdb file -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] REMD system blowing up

Hi all, I would like to know if there is a way to figure out which of the replica is exploding during REMD simulation? I am running REMD for 54 replicas and the system is exploding with just one step14495b.pdb and step14495c.pdb files. Does this mean there is just one replica that is exploding?

Re: [gmx-users] REMD and distance restraints problem in gmx 4.6.7

Hi, On Fri, Sep 18, 2015 at 6:27 AM Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > Dear Users: > > I have a system with many distance restraints, designed to maintain > helical character, e.g.: > [ distance_restraints ] > 90 33 1 1 2 2.745541e-01 3.122595e-01 999 1.0 > 97 57 1 2 2

Re: [gmx-users] REMD and distance restraints problem in gmx 4.6.7

raham <mark.j.abra...@gmail.com> Sent: 18 September 2015 04:11 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] REMD and distance restraints problem in gmx 4.6.7 Hi, On Fri, Sep 18, 2015 at 6:27 AM Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > Dear Users: > >

[gmx-users] REMD and distance restraints problem in gmx 4.6.7

Dear Users: I have a system with many distance restraints, designed to maintain helical character, e.g.: [ distance_restraints ] 90 33 1 1 2 2.745541e-01 3.122595e-01 999 1.0 97 57 1 2 2 2.876300e-01 2.892921e-01 999 1.0 114 73 1 3 2 2.704403e-01 2.929642e-01 999 1.0 ... Distance restraints are

[gmx-users] REMD temperature trajectory

Dear Gromacs user, I performed a REMD simulation and I want to analyse my result per temperature. I am interested at looking the trajectory for the lowest and the highest temperature. I am used to perform REMD with Amber and I realised that Amber exchanges temperature during the

Re: [gmx-users] REMD mdrun_mpi error

Hi Mark, I tried to run an individual tpr file and it crashed: Double sids (0, 1) for atom 26 Double sids (0, 1) for atom 27 Double sids (0, 1) for atom 28 Double sids (0, 1) for atom 29 Double sids (0, 1) for atom 30 Double sids (0, 1) for atom 31 Double sids (0, 1) for atom 32 Double sids (0,

Re: [gmx-users] REMD mdrun_mpi error

Hi, Do your individual replica .tpr files run correctly on their own? Mark On Mon, Jun 22, 2015 at 3:35 PM Nawel Mele nawel.m...@gmail.com wrote: Dear gromacs users, I am trying to simulate a ligand using REMD method in explicit solvent with the charmm force field. When I try to

[gmx-users] REMD with different structures

Hi I am trying to do NVT REMD simulations with gromacs. I have 60 replicas and each of them have different starting structure . The starting structures have same number of atoms but slightly different volume and pressure. I was able to run these simulations but I want to know if having

[gmx-users] REMD mdrun_mpi error

Dear gromacs users, I am trying to simulate a ligand using REMD method in explicit solvent with the charmm force field. When I try to equilibrate my system I get this error : Double sids (0, 1) for atom 26 Double sids (0, 1) for atom 27 Double sids (0, 1) for atom 28 Double sids (0, 1) for atom

[gmx-users] REMD exchange probabilities

Dear list, Using an exchange probability of 0.25 and temperature range 293-370 K, I calculated number of replicas using the server. However, when I did first run and tried exchanging replicas every 500 steps (1 ps), I don't think the exchange probabilities make sense in particular replicas 15

Re: [gmx-users] REMD: mdrun_mpi crash with segmentation fault (but mpi is working)

On 2/10/15 7:35 AM, Felipe Villanelo wrote: Absolutely nothing is written in the log file, just the citations That indicates that the simulation systems are totally unstable and crash immediately. Test by running each job individually (not as part of REMD) and see if you can do any

Re: [gmx-users] REMD: mdrun_mpi crash with segmentation fault (but mpi is working)

Absolutely nothing is written in the log file, just the citations Felipe Villanelo Lizana Bioquímico Laboratorio de Biología Estructural y Molecular Universidad de Chile 2015-02-03 10:01 GMT-03:00 Felipe Villanelo el.maest...@gmail.com: Hi, I trying to learn REMD following the tutorial on

Re: [gmx-users] REMD: mdrun_mpi crash with segmentation fault (but mpi is working)

Hi, What was the last thing written to the log files? Mark On Tue, Feb 3, 2015 at 2:01 PM, Felipe Villanelo el.maest...@gmail.com wrote: Hi, I trying to learn REMD following the tutorial on gromacs page

[gmx-users] REMD: mdrun_mpi crash with segmentation fault (but mpi is working)

Hi, I trying to learn REMD following the tutorial on gromacs page http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham,_Session_1B on a 4-cores computer. However when I try to use the command:

Re: [gmx-users] REMD tutorial

On Thu, Aug 21, 2014 at 8:01 AM, shahab shariati shahab.shari...@gmail.com 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

Re: [gmx-users] REMD: A small bug in repl_ex.c and a related question

On Fri, Jun 27, 2014 at 5:27 AM, Suman Chakrabarty chakrabarty.su...@gmail.com wrote: Hello! 1. It seems I have encountered a minor bug (?) in repl_ex.c for version 4.6.x (for NPT simulations only): Line 880 (in version 4.6.5): fprintf(fplog, dpV = %10.3e d = %10.3e\nb,

  1   2   >