Re: [gmx-users] REMD

dear Mark, Thank you very much for your prompt reply. I try to use parallel computing. It works fine. for example: grompp -f -c -p -o replica0 -np 2 -sort -shuffle to get replica0.tpr then, mdrun_mpi -np 2 -s replica0.tpr The error message mentioned in the previo

Re: [gmx-users] REMD

> Dear gmx users: > > I am trying to run REMD with two replicas (for testing). I used > grompp -f -c -p -o replica0 to get replica0.tpr > grompp -f -c -p -o replica1 to get replica1.tpr > > then used > mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica > -v -N 2 > to run it.

[gmx-users] REMD

Dear gmx users: I am trying to run REMD with two replicas (for testing). I used grompp -f -c -p -o replica0 to get replica0.tpr grompp -f -c -p -o replica1 to get replica1.tpr then used mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica -v -N 2 to run it. I got an error me

[gmx-users] (error in MD run)

Hi, I have a problem in md run: “Fatal error: realloc for nlist->jjnr (160825344 bytes, file ns.c, line 368, nlis t->jjnr=0x0x64960020): No such file or directory” My .tpr and .top files are including:   [ molecules ] ; Compound    #mols Protein     1 SOL 686247 NA+

RE: [gmx-users] Using Pull code with Coarse grain model

Mohan, What happens if you run it without using the pull code? i.e. is it a MD parameter problem or something to do with the pull code specifically. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Roy

Re: [gmx-users] MD run error

Hi again !   Thanks a lot for your help. its a great learning experience since am new to GROMACS. Well I have made a membrane and i have put two water boxes on top of the membrane.These three structures were combined in to one and i wanted to run energy minimization on the resulting structure.   I 

[gmx-users] Using Pull code with Coarse grain model

Hi all, I am trying to use the pull code for constrained force method in a coarse grain dppc bilayer model developed by Dr. S.J. Marrink. But I am getting error message Warning: pressure scaling > 1% . The problem persist even after I changed the tau_p from 1.0 to 1.5. Has anyone had any success on

Re: [gmx-users] seperating bilayers (again)

What is your van der Waals cut-off distance? From our experience years ago, we sometimes saw this if our van der Waals cut-off was too short; i.e., less than 15 angstroms. That seems long, since it falls off as sixth power, but because the long-range van der Waals is all attractive, there is n

Re: [gmx-users] Local electric field after enerygrp_exl

have some test on your own? Yang Ye Yinghong wrote: > Dear users: > If I excluded the interactions between two groups through defining > "energygrp_excl=Group1 Group2" in mdp file, > I am sure no interactions between them during simulation. However, how > about the local electric field between >

Re: [gmx-users] Re: problem while running grompp Pocition restrined dynamics

It is not how to increase it but how to avoid it. Try to have longer equilibration time before production MD. Yang Ye santosh naik wrote: Warning: 1-4 interaction between 1124 and 1137 at distance 1.973 which is larger than the 1-4 table size 1.000 nm i got this warning while running the simula

Re: [gmx-users] MSD and self diffusion

Hi Roman. Let me guess... in theory the MSD should start non-linear and after some time become linear until the end of simulation but the g_msd output starts linear and after become anything. I don´t know if I´m correct about your results but this was the results I had when trying to calcula

[gmx-users] Re: problem while running grompp Pocition restrined dynamics

Warning: 1-4 interaction between 1124 and 1137 at distance 1.973 which is larger than the 1-4 table size 1.000 nm i got this warning while running the simulation how could i increase it On 4/12/06, santosh naik <[EMAIL PROTECTED]> wrote: > 7/out7.gro is the out put of mdrun i have run for em > >

Re: [gmx-users] MSD and self diffusion

Hi Roman,It would help more if you mention what it does look like and why you would think it should look otherwise. Maybe you can link us an image of the graph?Haven't heard of strange behaviour concerning g_msd recently.., but haven't used it myself lately. Cheers,TsjerkOn 4/12/06, Roman Holomb <[

[gmx-users] MSD and self diffusion

Dear all, I have strange MSD graphs when I use g_msd for trajectory analysis.. It not look like (<|r(t)-r(0)|^2>) The simulation time was 5ns. Have someone problems with using g_msd? Thanks. /Roman ___ gmx-users mailing listgmx-users@grom

[gmx-users] Re: problem while running grompp Pocition restrined dynamics

7/out7.gro is the out put of mdrun i have run for em On 4/12/06, X.Periole <[EMAIL PROTECTED]> wrote: > > Your topology file does not correspond to the coordinate > file. You got to check both of them but the error is > certainly coming from the topology file. Not that you need > to include the i

Re: [gmx-users] configure: error: conditional "am__fastdepCXX" was never defined.

Hi, On Apr 12, 2006, at 9:41 AM, Florian Haberl wrote: Does anyone have a clue from what this error is and how it can be fixed? Update your gromacs version to 3.3.1 configure: error: conditional "am__fastdepCXX" was never defined Perhaps you have to update your system too, automake and

Re: [gmx-users] problem while running grompp Pocition restrined dynamics

Your topology file does not correspond to the coordinate file. You got to check both of them but the error is certainly coming from the topology file. Not that you need to include the ions.itp file after incerting the ions. It is better to insert the ions in the solvent Temp bath and not in a

[gmx-users] Re: problem while running grompp Pocition restrined dynamics

no i have given the right path only even i have checked the top file 2 do that first md run can make any harmful changes in top file On 4/12/06, Mark Abraham <[EMAIL PROTECTED]> wrote: > santosh naik wrote: > > hi guys > > i am working with the spider toxin protein and as mentioned early i > > w

Re: [gmx-users] problem while running grompp Pocition restrined dynamics

santosh naik wrote: hi guys i am working with the spider toxin protein and as mentioned early i was unable 2 over come this process below i have mentioning my problem in detail Thanks for that. It looks OK to me. I've snipped out the lines where you mention the .top file grompp -f em.mdp -c

Re: [gmx-users] problem while running grompp Pocition restrined dynamics

hi, On Wednesday 12 April 2006 09:41, santosh naik wrote: > hi guys > i am working with the spider toxin protein and as mentioned early i > was unable 2 over come this process > > below i have mentioning my problem in detail > > first i take the protein and run the pdb2 gmx command under the > gr

[gmx-users] problem while running grompp Pocition restrined dynamics

hi i am working with the spider toxin protein and as mentioned early i was unable 2 over come this process below i have mentioning my problem in detail first i take the protein and run the pdb2 gmx command under the gromacs force field pdb2gmx -f spider.pdb -o 1/out1.gro -p 1/out1.top editconf -bt

Re: [gmx-users] configure: error: conditional "am__fastdepCXX" was never defined.

hi On Wednesday 12 April 2006 01:06, Vanessa Oklejas wrote: > Hi everybody, > > I've been trying to compile gromacs-3.1.4 onto a linux server with > Red Hat v 7.3 OS. I was able to compile the fftw library without > incident, but when I issue the configure command (>./configure > --prefix=/home/v

[gmx-users] problem while running grompp Pocition restrined dynamics

hi guys i am working with the spider toxin protein and as mentioned early i was unable 2 over come this process below i have mentioning my problem in detail first i take the protein and run the pdb2 gmx command under the gromacs force field pdb2gmx -f spider.pdb -o 1/out1.gro -p 1/out1.top the