Re: [gmx-users] blue gene running error

hello Makr: thanks a lot for kind reply. From the link you you mentioned, it seems that this problem comes from the MD system itself. However, it goes well in my workstation. Moreover, I visualized and analyzed the results from my workstation running, everything goes well. I don't find any

Re: [gmx-users] blue gene running error

hello Mar: thanks a lot for kind reply. From the link you you mentioned, it seems that this problem comes from the MD system itself. However, it goes well in my workstation. Moreover, I visualized and analyzed the results from my workstation running, everything goes well. I don't find any p

Re: [gmx-users] blue gene running error

On 28/04/2012 2:04 PM, Albert wrote: hello: I am running NPT on a blue gene cluster, but the jobs always failed with following messages. However, everything goes well if I run it on my local cluster: Systems with marginally stable initial conditions can do this. See http://www.gromacs.org/

[gmx-users] blue gene running error

hello: I am running NPT on a blue gene cluster, but the jobs always failed with following messages. However, everything goes well if I run it on my local cluster: ---log--- ol 0.66! imb F 6% pme/F 0.45 step 900, will finish Mon Apr 30 04:46:31 20

RE: [gmx-users] SWM4_DP water on graphite surface

Thank Mark, I did not freeze the SOL. My graphite surface blew up. The system is: A water film is about 6A from graphite surface. The water film is equilibrated before placed on graphite surface. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraha

Re: [gmx-users] SWM4_DP water on graphite surface

On 28/04/2012 10:54 AM, Ho, Tuan A. wrote: Thank Mark, I freeze the SOL because I would like to check if it is because of SOL bad contact. You can't do a dynamical simulation with zero degrees of freedom. However, it turns out that the graphite deformation is the problem. Under what c

RE: [gmx-users] SWM4_DP water on graphite surface

Thank Mark, I freeze the SOL because I would like to check if it is because of SOL bad contact. However, it turns out that the graphite deformation is the problem. My friend asks me to use only one processor, and it is running well (no SOL freeze). Hopefully, after I got the final configuration f

Re: [gmx-users] SWM4_DP water on graphite surface

On 28/04/2012 3:33 AM, Ho, Tuan A. wrote: Dear Gromacs users, I would like to simulate a thin film of SWM4_DP water on graphite surface. First, I equilibrate the water only (run very well), then I add a graphite surface on it. I freeze the graphite surface but the graphite surface acted craz

Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF

Oh, I see. I did inserted only the provided values from CHARMM ff prm file. Now I'll do some testing... Thanks Peter, ---  Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics & Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São P

Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF

btw you only need explicit 1-4 for charmm when the 1,4 from the original charmm prm is actually different/specified (i.e. non-conjugated carbons) -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. "Ricardo O. S. Soares" wrote: Hi Mark, yeah, I'll try it. Thanks for yo

Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF

Hi Mark, yeah, I'll try it. Thanks for your reply, Ricardo. > > De: Mark Abraham >Para: Discussion list for GROMACS users >Enviadas: Sexta-feira, 27 de Abril de 2012 10:43 >Assunto: Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in >CHAR

[gmx-users] SWM4_DP water on graphite surface

Dear Gromacs users, I would like to simulate a thin film of SWM4_DP water on graphite surface. First, I equilibrate the water only (run very well), then I add a graphite surface on it. I freeze the graphite surface but the graphite surface acted crazily after a few time step (graphite surface de

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

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Justin and Anirban, My phase-2 equibration run was completed and I could see SOL molecules moved close to the head groups of lipids. Now, I'm confident that I can apply this rocedure on other proteins as well. Thank you so much both you for walking along through the session. Bala S -- View this

Re: [gmx-users] TRR file with nstxout= 0

On 4/27/12 12:09 PM, Steven Neumann wrote: On Fri, Apr 27, 2012 at 4:38 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote: On 4/27/12 11:34 AM, Steven Neumann wrote: On Fri, Apr 27, 2012 at 4:28 PM, Justin A. Lemkul mailto:jalem...@vt.edu>

Re: [gmx-users] TRR file with nstxout= 0

On Fri, Apr 27, 2012 at 4:38 PM, Justin A. Lemkul wrote: > > > On 4/27/12 11:34 AM, Steven Neumann wrote: > >> >> >> On Fri, Apr 27, 2012 at 4:28 PM, Justin A. Lemkul > > wrote: >> >> >> >>On 4/27/12 11:22 AM, Steven Neumann wrote: >> >>Dear Gmx Users, >> >>

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Hi Justin and Anirban, I've seen that most of the SOL molecules movin towards the head groups after NVT equilibrium run as mentioned in Justin's. I'm wiating for my NPT run to complete. Hopefully I can see all of them aliging over the headgroups. Thanks -- View this message in context: http://

Re: [gmx-users] TRR file with nstxout= 0

On 4/27/12 11:34 AM, Steven Neumann wrote: On Fri, Apr 27, 2012 at 4:28 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote: On 4/27/12 11:22 AM, Steven Neumann wrote: Dear Gmx Users, I am running 2 us simulation in implicit solvent model: define= -DP

Re: [gmx-users] TRR file with nstxout= 0

On Fri, Apr 27, 2012 at 4:28 PM, Justin A. Lemkul wrote: > > > On 4/27/12 11:22 AM, Steven Neumann wrote: > >> Dear Gmx Users, >> >> I am running 2 us simulation in implicit solvent model: >> >> define= -DPOSRES >> integrator= sd; leap-frog integrator >> nsteps= 50

Re: [gmx-users] TRR file with nstxout= 0

On 4/27/12 11:22 AM, Steven Neumann wrote: Dear Gmx Users, I am running 2 us simulation in implicit solvent model: define= -DPOSRES integrator= sd; leap-frog integrator nsteps= 5 ; 0.004 * 5= 2 us dt= 0.004 ; 4 fs ; Output contro

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] How to use -tablep mdrun option?

On 28/04/2012 12:19 AM, Marcelo Lopez wrote: Thank you very much Mark, I have already in my topology files nrexcl = 3 and gen-pairs = no Please enlight me... Does this mean that all the 1-4 interactions (I have tabulated bonds, angles and dihedrals) are zero? Look at what the .log file repo

[gmx-users] Re: double precision energy minimization show zero pressure in gromacs 4.5.5

Can anyone from development comment on this? I see that now 4.6 is coming out ... if this is a bug in the code, it would be nice if it's fixed in 4.6. Greg On Thu, Apr 26, 2012 at 11:00 AM, Yongchul Chung wrote: > Hi all, > > I am carrying out energy minimization on bulk polymer system (N~2

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

On Fri, Apr 27, 2012 at 7:37 PM, Justin A. Lemkul wrote: > > > On 4/27/12 10:00 AM, Bala S wrote: > >> Anirban, >> >> Exactly.. That's the gap (either side of the leaflets) I was mentioning >> about. I'll try EM and check itagain. >> >> > EM won't fill in solvent gaps. If you're using my protoco

Re: [gmx-users] How to use -tablep mdrun option?

Thank you very much Mark, I have already in my topology files nrexcl = 3 and gen-pairs = no Please enlight me... Does this mean that all the 1-4 interactions (I have tabulated bonds, angles and dihedrals) are zero? Because I'm trying to put a strong repulsive part in the non-bonding potentials

Re: [gmx-users] Extract pullF from trajectory

On Fri, Apr 27, 2012 at 2:53 PM, Thomas Schlesier wrote: > Am 27.04.2012 15:31, schrieb gmx-users-requ...@gromacs.org: > >> Hi Gmx Users, >> >> I run umbrella sampling simulation and for one window I lost my files: >> pullf.xvg and pullx.xvg. >> Is there any way to extract it based on the trajecto

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

On 4/27/12 10:00 AM, Bala S wrote: Anirban, Exactly.. That's the gap (either side of the leaflets) I was mentioning about. I'll try EM and check itagain. EM won't fill in solvent gaps. If you're using my protocol for increasing the C radius in vdwradii.dat, then a small gap is normal and

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Anirban, Exactly.. That's the gap (either side of the leaflets) I was mentioning about. I'll try EM and check itagain. Thanks. -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933996.html Sent from the GROMACS Users Forum mailing l

[gmx-users] Extract pullF from trajectory

Am 27.04.2012 15:31, schrieb gmx-users-requ...@gromacs.org: Hi Gmx Users, I run umbrella sampling simulation and for one window I lost my files: pullf.xvg and pullx.xvg. Is there any way to extract it based on the trajectory from this window? Steven Should be possible, but you will be limited

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

On Fri, Apr 27, 2012 at 7:00 PM, Bala S wrote: > Anirban, > > Thank you. You guys are doing miracles with the biomolecules and solving > almost all of my problems. > > I have followed your suggestion and could see now some more SOL molecules > by > increasing the z value. > > But I am seeing a su

Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF

On 27/04/2012 5:21 AM, Ricardo O. S. Soares wrote: Dear users, In GROMACS, does CHARMM36 ff, calculate eventual 1-4 interactions that are absent from the [pairtypes] section of the ffnonbonded.itp file? I ask this because I'm converting cholesterol parameters from CHARMM36c to gmx format, and

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

Re: [gmx-users] How to use -tablep mdrun option?

On 27/04/2012 11:07 PM, Marcelo Lopez wrote: Hi all, I'm trying to run a coarse grained system with tabulated non-bonding potentials for 3 kind of particles. I need to set all the 1-4 interactions to zero Why not use nrexcl = 3 in your [moleculetype] like the example in manual 5.7.1? (and pro

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Anirban, Thank you. You guys are doing miracles with the biomolecules and solving almost all of my problems. I have followed your suggestion and could see now some more SOL molecules by increasing the z value. But I am seeing a substantial gap between the surface of the lipid bilayer and added S

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

On Fri, Apr 27, 2012 at 6:31 PM, Bala S wrote: > Justin, > > OOPS!! > Sorry for that.. Now I could realize it. > Following up.. I have done further iterations with inflategro and reached > 0.62 nm^2 which similar to what you have explained in the tutorial. > > Now, I could see the lipid bilayer r

[gmx-users] How to use -tablep mdrun option?

Hi all, I'm trying to run a coarse grained system with tabulated non-bonding potentials for 3 kind of particles. I need to set all the 1-4 interactions to zero but I can't find in the manual or elsewhere hot to construct the tables for the -tablep option of mdrun. I've readed a thread in the mail

[gmx-users] Extract pullF from trajectory

Hi Gmx Users, I run umbrella sampling simulation and for one window I lost my files: pullf.xvg and pullx.xvg. Is there any way to extract it based on the trajectory from this window? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Ple

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Justin, OOPS!! Sorry for that.. Now I could realize it. Following up.. I have done further iterations with inflategro and reached 0.62 nm^2 which similar to what you have explained in the tutorial. Now, I could see the lipid bilayer really shrinked and no SOL molecules are seen in between. Now th

[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] Re: GPCR MD Tutorial Using GROMACS (URL)

On 4/27/12 8:38 AM, Bala S wrote: Thanks Justin and Anirban for taking this long in TM simulations. I'm following Justin's tutorial majorly and taking some clues from Anirban's too when I need further clarification. From both of your guidelines I could understand wht I should be doing before

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Thanks Justin and Anirban for taking this long in TM simulations. I'm following Justin's tutorial majorly and taking some clues from Anirban's too when I need further clarification. >From both of your guidelines I could understand wht I should be doing before solvating the system. Now, I have a q

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

On Fri, Apr 27, 2012 at 4:59 PM, Justin A. Lemkul wrote: > > > On 4/27/12 6:40 AM, Bala S wrote: > >> Thanks for the reply. >> >> I'm following the tutorial. >> >> > Please clarify whether you're using Anirban's or mine. Now that two > exist, people will have to be a fair bit more specific :) >

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

On 4/27/12 6:40 AM, Bala S wrote: Thanks for the reply. I'm following the tutorial. Please clarify whether you're using Anirban's or mine. Now that two exist, people will have to be a fair bit more specific :) In your system, to solvate it you have the values that was used during the p

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Thanks for the reply. I'm following the tutorial. In your system, to solvate it you have the values that was used during the protien insertion into the bilayer. Following it, I have used the following commandfor my system where the protein is very much smaller than the length of the bilayer. $ e

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

On 4/27/12 6:04 AM, Anirban Ghosh wrote: On Fri, Apr 27, 2012 at 3:27 PM, Bala S mailto:think_bey...@aol.com>> wrote: Thank you for that clarification. I found that there were SOL molecules in .top file. I could run the EM now. Coming to the Solvation step, I'm facing a problem

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

On Fri, Apr 27, 2012 at 3:27 PM, Bala S wrote: > Thank you for that clarification. > > I found that there were SOL molecules in .top file. I could run the EM now. > > Coming to the Solvation step, I'm facing a problem. > > I have made the mentioned change (0.15 to 0.375 for C) in the vdwradii.dat

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Thank you for that clarification. I found that there were SOL molecules in .top file. I could run the EM now. Coming to the Solvation step, I'm facing a problem. I have made the mentioned change (0.15 to 0.375 for C) in the vdwradii.dat locally. While adding the solvent molecules, what command

Re: [gmx-users] Regarding errors

On Fri, Apr 27, 2012 at 3:17 PM, seera suryanarayana wrote: > Respected Sir, > > While i am running gromacs software i am getting the > following error.Kindly knowing me how to over come the error. > > Fatal error: > numbe

[gmx-users] Regarding errors

Respected Sir, While i am running gromacs software i am getting the following error.Kindly knowing me how to over come the error. Fatal error: number of coordinates in coordinate file (1cys_ion.gro, 99670)

Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

On Fri, Apr 27, 2012 at 1:01 PM, Bala S wrote: > Dear Justin > > Thanks for the explanation. > > I am following your tutorial of KALP membrane simulation. I am stuck in > between two steps of InflateGRO. After the first step, the tutorial > requests > to perform EM. Should I be running grompp wit

Re: [gmx-users] Acpype doubts

Hi Thales, Amber 1.5? You mean Amber12 and ambertools12? I haven't test with them yet, but it would help me if you run in the debug mode and post the output here for me: acpype -di proteinname.mol2 -c user Thanks, Alan On 26 April 2012 19:02, Thales Kronenberger wrote: > I configure Amber1

Re: [gmx-users] Regarding errors

On 27/04/2012 5:07 PM, seera suryanarayana wrote: Respected Sir, While i am running the gromacs software i am getting the following error.Kindly knowing how to over come the error. Fatal error: Residue 'CCN' not found in residue topology database http://www.gromacs.org/Do

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Dear Justin Thanks for the explanation. I am following your tutorial of KALP membrane simulation. I am stuck in between two steps of InflateGRO. After the first step, the tutorial requests to perform EM. Should I be running grompp with new system_inflated.gro file to generate a new .tpr file for

[gmx-users] Regarding errors

Respected Sir, While i am running the gromacs software i am getting the following error.Kindly knowing how to over come the error. Fatal error: Residue 'CCN' not found in residue topology database SURYANARAYANA SEERA, PhD student. -- gmx-users mailing listgmx-users@grom