Re: [gmx-users] topology for small peptide using amber03

2013-11-28 Thread Mark Abraham
PDB format has fixed column widths. You cannot edit it correctly unless you preserve the layout - e.g. replace deleted characters with spaces. Mark On Nov 28, 2013 4:26 AM, kolnkempff kolnkem...@gmail.com wrote: /I am trying to use pdb2gmx to get a topology for a very simple peptide that has

Re: [gmx-users] step 0Segmentation fault: 11

2013-11-28 Thread Mark Abraham
Huge forces lead to crazy displacements whose next forces are looked up outside the boundaries of your table, which leads to a segmentation fault. GROMACS doesn't waste its time checking for this, since that would hurt everyone's performance and gain only a descriptive error that something is

Re: [gmx-users] step 0Segmentation fault: 11 (Mark Abraham)

2013-11-28 Thread ERASTOVA V.
Thank you, Mark. It makes sense. I am using FF developed by other group, that was run in Discover before. I am not sure I like how the plots of potentials look. V Huge forces lead to crazy displacements whose next forces are looked up outside the boundaries of your table, which leads to a

[gmx-users] free energy landscape

2013-11-28 Thread aixintiankong
Dear, i want to make a free energy landscape with respect to Rg and RMSD. First i get the rmsd.xvg by g_rms and then get the Rg.xvg file by g_gyrate. And the i merge the rmsd value and Rg value into one file with two column, then i use the g_sham command to got the free energy landscapes.

[gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Mahboobeh Eslami
Hi GMX Users, please help me I am trying to begin a simulation of a protein and ligand coplex by gromacs4.6.3. I am using AMBER99sb-ILDN force field and TIP4P water model. However, I am facing a problem in the ion adding step. when I issue the grompp command to generate the necessary .tpr file

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Timo Graen
On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: Hi GMX Users, please help me I am trying to begin a simulation of a protein and ligand coplex by gromacs4.6.3. I am using AMBER99sb-ILDN force field and TIP4P water model. However, I am facing a problem in the ion adding step. when

Re: [gmx-users] Regarding soft core parameter: Relative solvation free energy calculation

2013-11-28 Thread Michael Shirts
Define large fluctuations. They might be physical large fluctuations! On Thu, Nov 28, 2013 at 1:19 AM, bipin singh bipinel...@gmail.com wrote: Hello All, I am trying to calculate relative solvation free energy for p-Cresol and p-Chlorophenol using Gromacs 4.6.3. I am using equispaced

[gmx-users] REMD on GPU

2013-11-28 Thread James Starlight
Dear Gromacs users! I'd like to perform replica exchange simulation For this I've made bash script which create n folders like replica-298 replica-312 replica-323 replica-334 ... replica-N with all files needed for simulation considted of specified mdp file with different ref_t value No I'd

Re: [gmx-users] free energy landscape

2013-11-28 Thread Justin Lemkul
On 11/28/13 7:20 AM, aixintiankong wrote: Dear, i want to make a free energy landscape with respect to Rg and RMSD. First i get the rmsd.xvg by g_rms and then get the Rg.xvg file by g_gyrate. And the i merge the rmsd value and Rg value into one file with two column, then i use the g_sham

Re: [gmx-users] Regarding soft core parameter: Relative solvation free energy calculation

2013-11-28 Thread bipin singh
Thanks for the reply. By large fluctuations, I mean the standard deviation of dh/dl values during the simulation at lambda 0.0 to 0.5 in comparison to lambda close to 1, when using sc-alpha=0.5 On Thu, Nov 28, 2013 at 7:27 PM, Michael Shirts mrshi...@gmail.com wrote: Define large

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Mahboobeh Eslami
dear timo Please send me further details. I'm not a professional. Thanks and regards On Thursday, November 28, 2013 4:28 PM, Timo Graen tgr...@gwdg.de wrote: On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: Hi GMX Users, please help me I am trying to begin a simulation of a

Re: [gmx-users] REMD on GPU

2013-11-28 Thread Mark Abraham
On Thu, Nov 28, 2013 at 3:01 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs users! I'd like to perform replica exchange simulation For this I've made bash script which create n folders like replica-298 replica-312 replica-323 replica-334 ... replica-N with all files

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Mohsen Ramezanpour
Maybe you should modify your .tpr file manually according to what you added in the previous sections! On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: dear timo Please send me further details. I'm not a professional. Thanks and regards On Thursday,

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Justin Lemkul
On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote: Maybe you should modify your .tpr file manually according to what you added in the previous sections! Manually modify a .tpr? How would one do that? The OP needs to provide the exact commands issued. The fatal error shown results from poor

Re: [gmx-users] For GMX implicit solvent MD

2013-11-28 Thread Justin Lemkul
On 11/28/13 9:31 AM, dxl...@hotmail.com wrote: Dear All, I'd like to do some implicit solvent MD with Gromacs. However, I meet a trouble. For instance, I have included gbsa.itp. when I used a SPC water molecule for Implicit Sovent MD,it goes very well. Then when I use two SPC water

Re: [gmx-users] Regarding soft core parameter: Relative solvation free energy calculation

2013-11-28 Thread bipin singh
I am mentioning below the average and standard deviation of dh/dl values at lambda=0.0 and lambda=1.0, for sc-alpha=0.5 Avg Std. lambda0.0-2.055812e+01 2.730571e+01 lambda1.07.086960e+017.670135e+00 On Thu, Nov 28, 2013 at 7:34 PM, bipin

Re: [gmx-users] parallelization of processors on single system/node using MPI

2013-11-28 Thread Szilárd Páll
Yes, you can besides the minor command-line interface differences, using MPI and thread-MPI works essentially the same way. http://www.gromacs.org/Documentation/Acceleration_and_parallelization#MPI.2c.c2.a0Thread-MPI -- Szilárd On Thu, Nov 28, 2013 at 11:07 AM, Richa Singh

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Mohsen Ramezanpour
Oh, I am sorry, I made a big mistake! :) Best Regards On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote: Maybe you should modify your .tpr file manually according to what you added in the previous sections! Manually

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Mohsen Ramezanpour
Dear Justin I meant modifying .top file after adding some ions and water molecules which could be equivalent to -p option as you mentioned. What do you think about this? Please let me know On Thu, Nov 28, 2013 at 6:37 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Oh, I am

Re: [gmx-users] Regarding soft core parameter: Relative solvation free energy calculation

2013-11-28 Thread Michael Shirts
It's very possible that this is entirely physical. dh/dl fluctuates a lot. You may want to look at graphs of dh/dl after a few 10's of ps to see if it looks reasonable. On Thu, Nov 28, 2013 at 10:04 AM, bipin singh bipinel...@gmail.com wrote: I am mentioning below the average and standard

Re: [gmx-users] AMBER ff10 with Gromacs

2013-11-28 Thread Thomas Piggot
In addition to where Szilard said to look, you can also try looking for force fields on the user contributions part of the GROMACS website: http://www.gromacs.org/Downloads/User_contributions/Force_fields If you need to use AMBER99SB force field with the ParmBSC0 nucleic acid parameters, this

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Justin Lemkul
On 11/28/13 10:13 AM, Mohsen Ramezanpour wrote: Dear Justin I meant modifying .top file after adding some ions and water molecules which could be equivalent to -p option as you mentioned. What do you think about this? That would be one possible solution, but it is not yet clear what the OP

Re: [gmx-users] AMBER ff10 with Gromacs

2013-11-28 Thread Szilárd Páll
PS: googling AMBER FF10 + GROMACS does give (at least) one relevant result: http://pubs.rsc.org/en/Content/ArticlePDF/2013/CP/c2cp44100d They may have something useful and may be willing to share (and it would certainly be useful to have it in the contrib FF section as well). Cheers, -- Szilárd

Re: [gmx-users] Regarding soft core parameter: Relative solvation free energy calculation

2013-11-28 Thread bipin singh
Thanks for you reply Prof. Shirts. I have plotted the dh/dl values (link mentioned below), but I am not sure whether the fluctuation is in acceptable range at lambda=0.0. Please have a look at the plot and let me know your thoughts. http://researchweb.iiit.ac.in/~bipin.singh/dhdl.png On Thu,

[gmx-users] Gemcitabine topolgy for OPLS

2013-11-28 Thread Andres Ortega
Hi, i´m trying to run a MD with Gemcitabine using OPLS /AA ff, to get the .itp, should i use topolgen , and then calculate the charges with gaussian ussing ChelpG charges, and replace it, i was wondering if this procedure is correct, algo i´m pretending , to study this molecule with a CNT, and a

[gmx-users] mdrun_mpi_d

2013-11-28 Thread Mahboobeh Eslami
Hi everybody i install gromacs 4.6.3  double precision and parallel what is the best correct command for  mdrun_mpi_d on single machine with multiple processors (core=8) thanks for your help -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] For GMX implicit solvent MD

2013-11-28 Thread dxli75
Dear all, I have changed the is.mdp file as following, However, the same error still can't be removed. What can I do for the simulation? title = spc water cpp = /usr/bin/cpp ;define = -DFLEXIBLE constraints = all-bonds integrator = md tinit = 0 dt = 0.002 ; ps ! nsteps = 2000 ;

Re: [gmx-users] mdrun_mpi_d

2013-11-28 Thread Chandan Choudhury
Dear Eslami, Gromacs 4.6.3 can automatically take up all the cores. If you want to run gromacs across the nodes. Then you need to compile using MPI. Detailed instruction is available here http://www.gromacs.org/Documentation/Installation_Instructions. Chandan -- Chandan kumar Choudhury NCL,

Re: [gmx-users] mdrun_mpi_d

2013-11-28 Thread Mahboobeh Eslami
hi i installed openmpi and i set -DGMX_MPI=ON in cmake command. are these casesenough? thanks On Friday, November 29, 2013 7:59 AM, Chandan Choudhury iitd...@gmail.com wrote: Dear Eslami, Gromacs 4.6.3 can automatically  take up all the cores. If you want to run gromacs across the