[gmx-users] remd

sir, I have a basic doubt about remd simulation. In remd is it possible to run 16 replicas in 8 processors? -- 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/Sear

RE: [gmx-users] REMD vs MD

; From: pqah...@gmail.com > To: gmx-users@gromacs.org > Subject: [gmx-users] REMD vs MD > > Hi all, > > I just want to ask you which is about REMD..I just understanding about > the MD simulation which is the basic one..If i have a several models > that i need to see the

[gmx-users] REMD vs MD

Hi all, I just want to ask you which is about REMD..I just understanding about the MD simulation which is the basic one..If i have a several models that i need to see the interaction between them is it okay to use MD?Or i need to use REMD instead? Thanks in advance, -- Best Regards, Nur Syafiq

Re: [gmx-users] REMD run on higher nodes.

On 8/5/13 6:36 AM, suhani nagpal wrote: Sir Yeah, I meant to use twice the hardware and i have already invoked mpiexec_mpt. the pbs script works fine if i start afresh mdrun of the tprs but if i extend the simulation run by -cpi filename -noappend the run doesnt take place. AFAIK, you can'

Re: [gmx-users] REMD run on higher nodes.

Sir Yeah, I meant to use twice the hardware and i have already invoked mpiexec_mpt. the pbs script works fine if i start afresh mdrun of the tprs but if i extend the simulation run by -cpi filename -noappend the run doesnt take place. On Mon, Aug 5, 2013 at 3:22 PM, Mark Abraham wrote: > Not

Re: [gmx-users] REMD run on higher nodes.

Not sure what you're asking, but if you're providing twice as much hardware, then invoke mpiexec_mpt suitably to tell it to use all of that. Then, if you invoke mdrun_mpi the same way as you do now, it will work out it can use twice as much hardware per replica. Mark On Mon, Aug 5, 2013 at 7:55 A

[gmx-users] REMD run on higher nodes.

Greetings I'm running REMD of 96 replicas where the run.pbs is the following: #!/bin/tcsh #PBS -S /bin/tcsh #PBS -l walltime=00:15:00 #PBS -q workq #PBS -l select=8:ncpus=12:mpiprocs=12 #PBS -l place=scatter:excl #PBS -V # Go to the directory from which you submitted the job cd $PBS_O_WORKDIR se

Re: [gmx-users] remd

What does gmxcheck say about them? On Aug 2, 2013 8:08 AM, "Shine A" wrote: > Sir, > > I did an 80 ns Remd simulation, after completion of the simulation > extended it up to 480 ns using tpbconv. Now the extended trajectories also > write on old trajectory files(traj.trr)? > -- > gmx-users m

[gmx-users] remd

Sir, I did an 80 ns Remd simulation, after completion of the simulation extended it up to 480 ns using tpbconv. Now the extended trajectories also write on old trajectory files(traj.trr)? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users *

Re: [gmx-users] remd

Hi! On 2013-07-12 07:58, Shine A wrote: Hi Sir, Is it possible to run an REMD simulation having 16 replicas in a cluster(group of cpu) having 8 nodes. Here each node have 8 processors. It is possible. If you have Gromacs (version >= 4.6) compiled with MPI and you specify the numbe

[gmx-users] remd

Hi Sir, Is it possible to run an REMD simulation having 16 replicas in a cluster(group of cpu) having 8 nodes. Here each node have 8 processors. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://w

Re: [gmx-users] remd

On 7/8/13 11:13 AM, Shine A wrote: Sir, I did an REMD for a peptide using implicit solvent model(8 replica 10 ns each).The experimental structure of peptide in water look like betasheet(from circular dichroism). But almost all conformations from trajectory look like alpha-helices.Then how

[gmx-users] remd

Sir, I did an REMD for a peptide using implicit solvent model(8 replica 10 ns each).The experimental structure of peptide in water look like betasheet(from circular dichroism). But almost all conformations from trajectory look like alpha-helices.Then how I can correlate experimental and theore

Re: [gmx-users] remd

Justin answered this question about average structures earlier today. Please read his answer. Mark On Tue, Jul 2, 2013 at 8:37 PM, Shine A wrote: > Sir, > > I trying to calculate ground state conformational ensemble of a > peptide by comparing experimental chemical shift and predicted chemi

[gmx-users] remd

Sir, I trying to calculate ground state conformational ensemble of a peptide by comparing experimental chemical shift and predicted chemical shifts.For that I did REMD simulation at 8 temperatures.Then using g_cluster clustered.Here is it reasonable to compare the chemical shift of average st

Re: [gmx-users] remd

On 02/07/13 12:10, Justin Lemkul wrote: On Tue, Jul 2, 2013 at 5:30 AM, Richard Broadbent < richard.broadben...@imperial.ac.uk> wrote: Not sure exactly what merging together means, for visualisation I generally use vmd as this supports gromacs files directly. If I understand correctly (and

Re: [gmx-users] remd

On Tue, Jul 2, 2013 at 5:30 AM, Richard Broadbent < richard.broadben...@imperial.ac.uk> wrote: > Not sure exactly what merging together means, for visualisation I > generally use vmd as this supports gromacs files directly. > > If I understand correctly (and the OP can clarify if I haven't), it so

Re: [gmx-users] remd

Not sure exactly what merging together means, for visualisation I generally use vmd as this supports gromacs files directly. Your problem might be to do with, using rlist, rcoulomb, and rvdw set to 0 is not the standard way to do an infinite cut-off normally you set them to -1 as in the manual

[gmx-users] remd

Sir, I did a 10 ns REMD simulation for a peptide, 8 replicas using amber force field.Then extracted pdb file from the trajectory and clustered using g_cluster. The I viewed the average structure of the cluster in pymol .But here the atoms are merged togather.why it happends?Is there any pro

Re: [gmx-users] REMD

Wrong way around. Decide what you want to observe and how you will measure it *before* you do a simulation. Now you have a chance of doing the right simulation. On point, check out out chapter 8 of the manual. Mark On Thu, Jun 27, 2013 at 7:17 AM, Shine A wrote: > Hai Sir, > > I did

[gmx-users] REMD

Hai Sir, I did an REMD simulation for an intrinsically disordered peptide.Then I extracted thousands of conformations(pdb) from trajectory. Now I want to compare experimental Chemical Shifts and NOE distance for the peptide with all these conformations.How can I do this? -- gmx-users

Re: [gmx-users] remd analysis

There's number of analysis tools briefly described in chapter 8 of the manual, and lots more detail in Appendix D. Have a look at what is there, and do your background reading of the literature to see the kinds of things people have done before you. Mark On Tue, Jun 25, 2013 at 1:18 PM, Shine A

[gmx-users] remd analysis

Sir, I did an remd simulation in implicit solvent for a peptide.I want to compare the NOE distances from NMR and various conformations from REMD output. Here how I get various conformations from remd trajectory? .Is any script is available to find distance between two particular atoms?.How

Re: [gmx-users] REMD run showing temperature range more than the equilibrated.

On Tue, Jun 4, 2013 at 12:51 PM, suhani nagpal wrote: > Hi all ! > > well, I'm working on REMD with 96 replicas, with temperature range 280K to > 425.04K. > > The NVT equilibration works well and graphs plotted show almost the > required temperature after equilibration. > > Then, after 3 ns of rem

[gmx-users] REMD run showing temperature range more than the equilibrated.

Hi all ! well, I'm working on REMD with 96 replicas, with temperature range 280K to 425.04K. The NVT equilibration works well and graphs plotted show almost the required temperature after equilibration. Then, after 3 ns of remd run , the edr -> xvg files show initial temperature atleast 40 -50 u

Re: [Spam:*****] [gmx-users] REMD analysis

They show which structure is in which ensemble, and the inverse. Look at the exchange events reported in the .log files and work out which is which. Mark On Thu, May 16, 2013 at 5:25 PM, bharat gupta wrote: > Sorry to ask this simple question but how to read the replica_index and > replica_tem

Re: [Spam:*****] [gmx-users] REMD analysis

Sorry to ask this simple question but how to read the replica_index and replica_temp files. I tried to search a lot but didn't find any information. As I have concatenated all log files and demuxed them. Here's first 10 lines from both files:- replica_index: 0 012345

Re: [Spam:*****] [gmx-users] REMD analysis

On Thu, May 16, 2013 at 2:04 PM, bharat gupta wrote: > Dear Sir, > > Here's the result of three different runs : > > Temperature distribution for three trials > > Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 > Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 > Rep

Re: [gmx-users] REMD analysis

Okay, now I can start with large production runs . On Thu, May 16, 2013 at 11:10 PM, XAvier Periole wrote: > > Indeed the Repeat-3 seems good. But I would guess you did not run too > long, right! That would explain the distribution of values! > > On May 16, 2013, at 2:04 PM, bharat gupta > wro

Re: [gmx-users] REMD analysis

Indeed the Repeat-3 seems good. But I would guess you did not run too long, right! That would explain the distribution of values! On May 16, 2013, at 2:04 PM, bharat gupta wrote: > Dear Sir, > > Here's the result of three different runs : > > Temperature distribution for three trials > > Re

Re: [Spam:*****] [gmx-users] REMD analysis

Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log fi

Re: [Spam:*****] [gmx-users] REMD analysis

You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta wrote: > Okay Sir, I will try two-three combinations this time and will report back > to you ... > > > On Thu, May 16, 2013 at 5:25 PM, XAvier Periole wrote: > >> >> An acc

Re: [Spam:*****] [gmx-users] REMD analysis

Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole wrote: > > An acceptance ratio of 0.2/0.3 is normally best. The problem with high > acceptance ratio is that it means that a large portion of the exchanges are >

Re: [Spam:*****] [gmx-users] REMD analysis

An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know p

Re: [Spam:*****] [gmx-users] REMD analysis

The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica

Re: [Spam:*****] [gmx-users] REMD analysis

The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta wrote: > Dear

Re: [Spam:*****] [gmx-users] REMD analysis

Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average prob

Re: [Spam:*****] [gmx-users] REMD analysis

You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the "Max drawing path length" i

[gmx-users] REMD analysis

Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exc

Re: [gmx-users] REMD average acceptance ratio

The values of exchange ratio look much better: they are similar over the range of temperatures. To reduce the ratio you have to increase the spacing between temperatures, which means increase the value of c in the formula I gave earlier. When you but the water in, the degrees of freedom (and

Re: [gmx-users] REMD average acceptance ratio

Dear Sir, I tried again with the following temp. ditribution, this time with 30 replicas (280 K -624K) and 500 ps simulation time for each one. 0 280 1 287.8 2 295.9 3 304.2 4 312.7 5 321.5 6 330.5 7 339.8 8 349.3 9 359.1 10 369.1 11 379.5 12 390.1 13 401.0 14 412.3 15 423.8 16 435.7 17 447.9 18

Re: [gmx-users] REMD average acceptance ratio

You are simulating in vacuo! Otherwise the temperature gaps are way too large … If you want to analyse the sampling at 300 K, I would suggest you start you first temperature lower, around 280/285 may be. At least to have your second temperature at 300 K. the value of c has absolutely not imp

Re: [gmx-users] REMD average acceptance ratio

Dear Sir, Here's the temperature range that I got form t-remd : 1 300 2 323.7 3 348.75 4 375.23 5 403.22 6 432.83 7 464.14 8 497.24 9 532.26 10 569.32 11 608.51 according the above equation c should be somewhere around 2.37. On Sat, May 11, 2013 at 11:10 PM, XAvier Periole wrote: > > Well, a

Re: [gmx-users] REMD average acceptance ratio

Well, actually things do not look so good. But is it possible that grace is actually no able to plot things correctly? You have line going throughout the plot from complete-left to complete-right! I am do not know what the t-rems calculator does but apparently it is not optimal in your case.

Re: [gmx-users] REMD Statistics

On Mon, May 6, 2013 at 3:48 AM, Kong xq wrote: > Hi Mark, > > > Thanks for your great help. I am sorry for the negligence to state the > variation value correctly( it should be 0.011 rather than 0.11). Does this > somewhat small value indicate the generalized equilibrium achieved? It might be

Re: [gmx-users] REMD Statistics

Hi Mark, Thanks for your great help. I am sorry for the negligence to state the variation value correctly( it should be 0.011 rather than 0.11). Does this somewhat small value indicate the generalized equilibrium achieved? I will search the papers you suggested. I am wondering whether the histog

Re: [gmx-users] REMD Statistics

On Sun, May 5, 2013 at 5:14 PM, Kong xq wrote: > Dear GMX users, > > I have some concerns about the statistics analysis of REMD which do > need your generous help. > > I performed a 50ns isothermal-isobaric REMD simulation with 64 replicas > spaning from 300K to 390K. Then I want to do so

[gmx-users] REMD Statistics

Dear GMX users, I have some concerns about the statistics analysis of REMD which do need your generous help. I performed a 50ns isothermal-isobaric REMD simulation with 64 replicas spaning from 300K to 390K. Then I want to do some statistics analysis for the results. First, I calculated t

Re: [gmx-users] REMD temperature spacing formula

On Thu, Apr 4, 2013 at 10:17 AM, Nikunj Maheshwari wrote: > Thanks for that link. > I have used it, but it only takes system size properties. It doesn't take > the potential energy values at all. > Actually it does, inasmuch as it uses parameters fitted to observed energy values, which you'd kno

Re: [gmx-users] REMD temperature spacing formula

Thanks for that link. I have used it, but it only takes system size properties. It doesn't take the potential energy values at all. I am looking if someone has used any alternate for temperature spacing generation? On Thu, Apr 4, 2013 at 1:16 PM, rama david wrote: > Dear > > http://folding.bmc.

Re: [gmx-users] REMD temperature spacing formula

Dear http://folding.bmc.uu.se/remd/ this may help you. With best regards On Thu, Apr 4, 2013 at 11:43 AM, Nikunj Maheshwari wrote: > Dear all, > > We are stuck at the last stage of running a successful REMD. > We have obtained average potential energy by fitting the energy values from > init

[gmx-users] REMD temperature spacing formula

Dear all, We are stuck at the last stage of running a successful REMD. We have obtained average potential energy by fitting the energy values from initial MD. We want to get the temperature spacing for 72 replicas, starting from 280K. We have gone through numerous papers, but none of them explain

Re: [gmx-users] REMD general protocol ...

Thank you justin. I will do the same. On Tue, Apr 2, 2013 at 10:06 PM, Justin Lemkul wrote: > > > On 4/2/13 9:24 AM, rama david wrote: > >> Thank you Massimo sandal, Justin and mark , >> >> I also goes through the article and GMX archive. >> But I confuse with the protocol ( I am naive in REMD

Re: [gmx-users] REMD general protocol ...

On 4/2/13 9:24 AM, rama david wrote: Thank you Massimo sandal, Justin and mark , I also goes through the article and GMX archive. But I confuse with the protocol ( I am naive in REMD . So I want to conform protocol from the Expert and experience person ) I will be grateful to you for your su

Re: [gmx-users] REMD general protocol ...

On 4/2/13 7:38 AM, Erik Marklund wrote: On 2 Apr 2013, at 13:30, Justin Lemkul wrote: On 4/2/13 7:13 AM, rama david wrote: Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly searc

Re: [gmx-users] REMD general protocol ...

Thank you Massimo sandal, Justin and mark , I also goes through the article and GMX archive. But I confuse with the protocol ( I am naive in REMD . So I want to conform protocol from the Expert and experience person ) I will be grateful to you for your suggestion. On Tue, Apr 2, 2013 at 6:4

Re: [gmx-users] REMD general protocol ...

I would look on some paper which temperature ranges and conditions (NPT/NVT) were used for systems of a similar size and with a similar aim. 2013/4/2 rama david > Dear friends , > Thank you justin and Mark for your suggestion > > I increases my temp range from 310-360 K > Now I get 20 replicas

Re: [gmx-users] REMD general protocol ...

Dear friends , Thank you justin and Mark for your suggestion I increases my temp range from 310-360 K Now I get 20 replicas . Is in such large temp range wlll it be good to use NPT. Would you tell me the temp differences in which box instability generally arises .. Is my working-flow right or

Re: [gmx-users] REMD general protocol ...

On 2 Apr 2013, at 13:30, Justin Lemkul wrote: > > > On 4/2/13 7:13 AM, rama david wrote: >> Dear friends, >> I am naive to the Replica exchange Molecular dynamics ( REMD). >> I have plan to use REMD for temp. 310-320 K to my system. >> I thoroughly search the Mailing-list Archive fo

Re: [gmx-users] REMD general protocol ...

On 4/2/13 7:13 AM, rama david wrote: Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly search the Mailing-list Archive for the REMD problem. It was a really helpful to start. My syst

[gmx-users] REMD general protocol ...

Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly search the Mailing-list Archive for the REMD problem. It was a really helpful to start. My system consist of peptide + water. I used the

Re: [gmx-users] REMD temperature spacing error

People often vary it to try to have an average exchange acceptance rate of a level they think is useful. But that is only a proxy for what they really want to achieve, which is replica flow, and it turns out that is a complex thing and often requires a irregular spacing anyway. Mark On Wed, Mar 1

Re: [gmx-users] REMD temperature spacing error

Sorry. I thought it was related to Boltzmann constt. Then how is 'k' calculated ? On Wed, Mar 13, 2013 at 8:17 PM, Mark Abraham wrote: > k is dimensionless. It does not relate to Boltzmann's constant. The > exponential spacing it produces would lead to replica exchange rates that > are constant o

Re: [gmx-users] REMD temperature spacing error

k is dimensionless. It does not relate to Boltzmann's constant. The exponential spacing it produces would lead to replica exchange rates that are constant over the T range, under certain assumptions (e.g. papers by David A Kofke). In practice, it normally would not lead to such rates. Whether const

Re: [gmx-users] REMD temperature spacing error

I think determining k in the equation is not clear. How is it related to a system size? If k=1/(kb.t) [kb=boltzmann constt], then for a given starting temperature, the temp. spacing will be the same. Is that correct? On Wed, Mar 13, 2013 at 5:02 PM, Mark Abraham wrote: > On Wed, Mar 13, 2013 at 1

Re: [gmx-users] REMD temperature spacing error

On Wed, Mar 13, 2013 at 11:24 AM, Nikunj Maheshwari < nixcrazyfor...@gmail.com> wrote: > Dear all. > > We are trying to run REMD on two proteins : 292 and 44 aa residues using > GROMACS 4.6. > We are unable to obtain the temperature spacing using REMD temperature > generator (http://folding.bmc.uu

Re: [gmx-users] REMD simulation

That looks very strange. Please file an issue at redmine.gromacs.orgincluding all your .tpr and .cpt, and assign it to me. Mark On Thu, Dec 13, 2012 at 1:07 PM, Kenny Bravo Rodriguez < ke...@mpi-muelheim.mpg.de> wrote: > Hi all, > > and thanks Mark, Chris and Xavier for your comments. > > I fina

[gmx-users] REMD simulation

Hi all, and thanks Mark, Chris and Xavier for your comments. I finally managed to run the REMD simulation but i can not restart the simulation or continue the simulation after it finished. I tried with a test system and run two replicas for just 20 ps. After it finished correctly i extended th

[gmx-users] REMD with umbrella sampling in Gromacs 4.5.5

Hi all, I've read some earlier posts in the forum about replica exchange combined with umbrella sampling but still not sure if the restrain potential defined in the pull code will be included in the exchange criterion: P(i<->j) = min (1, exp[ (beta_i-beta_j)*(U(Ri, Dj) + U(Rj,Di) - U(Ri,Di) - U(R

[gmx-users] REMD with umbrella sampling in Gromacs 4.5.5

Hi all, I've read some earlier posts in the forum about replica exchange combined with umbrella sampling but still not sure if the restrain potential defined in the pull code will be included in the exchange criterion: P(i<->j) = min (1, exp[ (beta_i-beta_j)*(U(Ri, Dj) + U(Rj,Di) - U(Ri,Di) -

Re: [gmx-users] REMD simulation

Virtual sites also have a hidden benefit - not only can you take a longer time step, but the width of the distribution of PE is relatively wider, so you can have higher exchange probability for the same temperatures. Mark On Tue, Nov 20, 2012 at 12:34 AM, Christopher Neale < chris.ne...@mail.utor

[gmx-users] REMD simulation

Xavier is right, except that you can also reduce the size of your system. You can take larger steps in temperature if you have fewer atoms. If you are using a cubic system, you can move to a rhombic dodecahedron. Even constraining all bonds will help a bit here (vs. harmonic bonds). There are

Re: [gmx-users] REMD simulation

Well either you use more replicas or you reduce the temperature range ... There is no way around! On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote: Dear All, i am trying to performed REMD simulations using Gromacs. My question is concerning the temperature distribution and the nu

[gmx-users] REMD simulation

Dear All, i am trying to performed REMD simulations using Gromacs. My question is concerning the temperature distribution and the number of replica. I need to run 24 replicas of my system with a temperature range of 290-400 K. How can I select the temperatures values for each replica? I tried t

Re: [gmx-users] REMD with Frozen DNA and Moving Protein

I second everything that Justin Lemkul wrote. This recent paper (C. A. Brackley, M. E. Cates, and D. Marenduzzo, Phys. Rev. Lett. 109:168103 (2012)) have a few weak points in my opinion, but demonstrate the artifacts that arise from freezing the DNA. Best, Erik 9 nov 2012 kl. 20.42 skrev Just

Re: [gmx-users] REMD with Frozen DNA and Moving Protein

On 11/9/12 9:02 AM, saber naderi wrote: Dear Gromacs Users, I would like to study structure of a positively charged protein in the vicinity of DNA. To do this, I want to perform replica exchange molecular dynamics simulations in which DNA is frozen and only the protein moves. This way I can ef

[gmx-users] REMD with Frozen DNA and Moving Protein

Dear Gromacs Users, I would like to study structure of a positively charged protein in the vicinity of DNA. To do this, I want to perform replica exchange molecular dynamics simulations in which DNA is frozen and only the protein moves. This way I can efficiently obtain the free energy landscape o

Re: [gmx-users] remd jobs failed

On 10/19/12 2:37 AM, Albert wrote: hello: I am trying to submit replica exchange jobs to cluster by following command, but failed: g_tune_pme_d -x -np 128 mdrun -s remd_.tpr -multi 16 -replex 1000 -reseed -1 -launch Here is the log file: -

Re: [gmx-users] remd jobs failed

Hi Albert, Please accept my apologies, I must have misread your e-mail. Effectively everything seems to be right in the command line and I am not able to understand either why you get the error. Good luck. Cheers, Davide On 19/10/12 7:54 PM, "Albert" wrote: >hello David: > >thanks for kind r

Re: [gmx-users] remd jobs failed

hello David: thanks for kind reply. The .tpr file was created by grompp in cluster and there is no problem for that. thank you very much Albert On 10/19/2012 08:52 AM, Davide Mercadante wrote: Hello, Basically is telling you that the output (.tpr) file that grompp should have created is not

Re: [gmx-users] remd jobs failed

Hello, Basically is telling you that the output (.tpr) file that grompp should have created is not there to be read. Check if grompp ran correctly and produced the wanted output. I suspect that it may have failed for some reasons. Hope this helps, Cheers, Davide On 19/10/12 7:37 PM, "Albert"

[gmx-users] remd jobs failed

hello: I am trying to submit replica exchange jobs to cluster by following command, but failed: g_tune_pme_d -x -np 128 mdrun -s remd_.tpr -multi 16 -replex 1000 -reseed -1 -launch Here is the log file: --- Program g_tune_pme_d, VERSION 4

[gmx-users] REMD queries

Hi friends , I am new to the REMD simulation. I read some thread from archive but they not clarify by queries that why I am asking you on forum I have following Queries: 1. I want to simulate protein by remd at physiological temp ( 310). So my initial temp of replica shou

Re: [gmx-users] REMD in explicit solvent

On 19/06/2012 5:55 PM, Esben Jannik Bjerrum wrote: Hi Gromacs Users I'm new to list, but hope to get a little help from someone experienced with setting up some replica exhange simulations in explicit solvent. It keeps exploding after app. 50 to 200 ps simulation time. It runs fine up to

[gmx-users] REMD in explicit solvent

Hi Gromacs Users I'm new to list, but hope to get a little help from someone experienced with setting up some replica exhange simulations in explicit solvent. It keeps exploding after app. 50 to 200 ps simulation time. It runs fine up to there, and then suddently one or a couple of atoms ge

RE: [gmx-users] REMD question

p.m. Para: Discussion list for GROMACS users Asunto: Re: [gmx-users] REMD question Gromacs already supports replica exchange -- what particularly are you implementing? Equilibration of pressure is always a good idea -- even if you are running NVT simulations, you want to get them to be at the

Re: [gmx-users] REMD question

Gromacs already supports replica exchange -- what particularly are you implementing? Equilibration of pressure is always a good idea -- even if you are running NVT simulations, you want to get them to be at the equilibrium volume for your system and temperature choice, which will require equilibra

[gmx-users] REMD question

Dear Gromacs Users, We are implementing REMD method in Gromacs in protein folding, in your web page you give some steps that don´t mention any step about NPT stabilization. This step is necessary to run REMD simulations? Thank you in advance, Nathalia -- gmx-users mailing list

Re: [gmx-users] REMD - low temperature ranges

If you are only interested in conformational sampling, then it makes sense to start at 300 K or even higher - maybe 320 K. The main reason for working at lower temperatures is if your system is unstable - eg. if you expect that the molecule will be mostly unfolded at 300 K and you want to sample

Re: [gmx-users] REMD - low temperature ranges

Hi Mark, Thanks for reply. The problem is that I have never found in the papers reasoning behind the the lower than 300K temperatures. Moreover, authors were interested in properties in 300K or above. I was wondering if this is not based on experience that REMD implemented in gromacs works better

Re: [gmx-users] REMD - low temperature ranges

On 27/04/2012 10:59 PM, Tomek Wlodarski wrote: Hi, I have notice that quite often people in REMD simulation use replicas in lower than 300K temp. Using for example temperature ranges from 250 to 450K I am wondering what is the purpose of those replicas. I have limited computational resources a

[gmx-users] REMD - low temperature ranges

Hi, I have notice that quite often people in REMD simulation use replicas in lower than 300K temp. Using for example temperature ranges from 250 to 450K I am wondering what is the purpose of those replicas. I have limited computational resources and I am wondering if for studing 175 aa protein is

Re: [gmx-users] REMD equilibration

23 mar 2012 kl. 11.37 skrev Justin A. Lemkul: > > > francesco oteri wrote: >> I understand, >> I am planning to run REMD between 300 and 600 K, so I think it is better >> equlibrating in NVT ensemble because at high temperature water evaporates, >> is it? > > Another very real concern is the

Re: [gmx-users] REMD equilibration

francesco oteri wrote: I understand, I am planning to run REMD between 300 and 600 K, so I think it is better equlibrating in NVT ensemble because at high temperature water evaporates, is it? Another very real concern is the stability of the simulations under NPT. At higher temperatures

Re: [gmx-users] REMD equilibration

emble, in which you want to carry out the > production REMD. > > Andreas > > >>>>>>>>>>>>>>> > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of francesco oteri > Sent: 23 March 2012 09:41 >

RE: [gmx-users] REMD equilibration

2 09:41 To: Discussion list for GROMACS users Subject: [gmx-users] REMD equilibration Dear gromacs users, I have to perform REMD simulation, but since it is the first time I apply this tecnique I have a question regarding system equilibration. As far as I know, befaore starting the REMD each replica

Re: [gmx-users] REMD equilibration

On 03/23/2012 10:41 AM, francesco oteri wrote: > Dear gromacs users, > I have to perform REMD simulation, but since it is the first time I apply > this tecnique I have a question regarding system equilibration. > As far as I know, befaore starting the REMD each replica has to be > equlibrated. The

[gmx-users] REMD equilibration

Dear gromacs users, I have to perform REMD simulation, but since it is the first time I apply this tecnique I have a question regarding system equilibration. As far as I know, befaore starting the REMD each replica has to be equlibrated. The equilibration has to be carried out in the NPT ensemble o

Re: [gmx-users] REMD error

The command I used this time :- mdrun_mpi mdrun -s prefix_.tpr -multi 5 -replex 100 Here's the error that I got :- Fatal error: The number of nodes (1) is not a multiple of the number of simulations (5) For more information and tips for troubleshooting, please check the GROMACS website at http:

Re: [gmx-users] REMD error

On 12/01/2012 5:45 PM, bharat gupta wrote: It says that "The number of cores must be a multiple of the number of replicas (given with |-multi|, which must equal the number of .tpr files i.e., 10 for the above general e

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