RE: [gmx-users] the box lengths

Thanks all, I know what's wrong now. I forgot to set pbc = xyz earlier. By the way, is it normal for test failure of the gmxtest? such as :~/src/gmxtest$ ./gmxtest.pl complex FAILED. Check files in field FAILED. Check files in tip4p FAILED. Check files in water 3 ou

RE: [gmx-users] the box lengths

Well... There is one line in try2-water.pdb, shows as below TITLE Protein REMARKTHIS IS A SIMULATION BOX CRYST1 86.185 86.185 86.185 60.00 60.00 90.00 P 1 1 Do you think something was wrong during genion -s try2-water.tpr -o try2-water-ions.pdb -conc 0.15 -neutral -pna

RE: [gmx-users] the box lengths

Well, there's ya problem :-) That specifies the box dimensions. Have a look at try2-water.pdb as well, then you should be able to pin down where the issue has arisen. Appears that one of those steps have failed to write the box dimensions. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition

RE: [gmx-users] the box lengths

There is none CRYST1 line in the file try2-water-ions.pdb. Thanks and regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au] Sent: Tuesday, June 15, 2010 1:24 PM

RE: [gmx-users] the box lengths

What is the contents of the CRYST1 line in the file try2-water-ions.pdb? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 --

Re: [gmx-users] the box lengths

Hi, Which version of gromacs was this again? There have been issues with pdb files being written without box (CRYST1) records, recorded in the archive. Check the output .pdb files, especially after calling genbox (grep "^CRYST1" file.pdb). Also, try the sequence always writing .gro files as output

RE: [gmx-users] the box lengths

Hi, That's very nice all of you. I was just worried that so many details would make things blur. pdb2gmx -f try2.pdb -o try2.gro -ignh then choose ffG53a6, below is the minim.mdp going to be used (more than once). //

RE: [gmx-users] the box lengths

As already mentioned by Justin, unless you copy and paste the commands and output you got, for us to see, we can only have stabs in the dark (which is what I did since you are missing lots of information on what you are actually doing) to what is actually going on. And don't type in the commands i

Re: RE: [gmx-users] the box lengths

- Original Message - From: #ZHAO LINA# Date: Tuesday, June 15, 2010 12:34 Subject: RE: [gmx-users] the box lengths To: Discussion list for GROMACS users > I used the same commands trying another proteins, but no > problems. So it's not the reason about the commands I used. Whether th

Re: [gmx-users] the box lengths

#ZHAO LINA# wrote: I used the same commands trying another proteins, but no problems. So it's not the reason about the commands I used. The problem is not whether or not your commands work for other systems, rather the fact that they are (for some reason) not working for this particular sy

Re: [gmx-users] sc_power

- Original Message - From: fancy2012 Date: Tuesday, June 15, 2010 12:28 Subject: [gmx-users] sc_power To: gmx-users > Hi GMX users, > What is the difference between the values of sc_power, 1 and > 2? Thanks very much! What is written in section 4.5.1 of the manual? Mark -- gmx-use

RE: [gmx-users] the box lengths

I used the same commands trying another proteins, but no problems. So it's not the reason about the commands I used. It did not contain the same number of molecules after genion when I changed the box size. The pressure coupling was not on, and I did not reach this steps. The problem I had just

[gmx-users] sc_power

Hi GMX users, What is the difference between the values of sc_power, 1 and 2? Thanks very much! All the best, fancy-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Pl

Re: [gmx-users] Positive Total energy

- Original Message - From: Thanasis Koukoulas Date: Tuesday, June 15, 2010 4:55 Subject: [gmx-users] Positive Total energy To: gmx-users@gromacs.org --- | > Hello > I have sent several emails and i am sorry. It is my last attempt

Re: [gmx-users] Re: gmx-users Digest, Vol 74, Issue 84 (anisotropic pressure coupling)

Shuangxing Dai wrote: Well, the final average pressure is not correct: * **<== ### ==>* * **< A V E R A G E S >* * **<== ### ==>* * * * Energies (kJ/mol)* * Buck.ham (SR) Coulomb (SR) Coul. recip. PotentialKinetic En.* *1.60633

Re: [gmx-users] question about [ pairs ] and interaction 1-4

- Original Message - From: Alan Date: Tuesday, June 15, 2010 0:22 Subject: [gmx-users] question about [ pairs ] and interaction 1-4 To: Gromacs > Hi there, > I mostly use ffamber and sometimes I look in oplsaa to understand how things > are implemented in gromacs (4.0.5)> > I have an

[gmx-users] Re: gmx-users Digest, Vol 74, Issue 84

Well, the final average pressure is not correct: * **<== ### ==>* * **< A V E R A G E S >* * **<== ### ==>* * * * Energies (kJ/mol)* * Buck.ham (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. * *1.60633e+06 -5.69243e+06 -3.4

Re: [gmx-users] xpm file

- Original Message - From: Carla Jamous Date: Monday, June 14, 2010 22:40 Subject: [gmx-users] xpm file To: Discussion list for GROMACS users > Hi everyone, > > please it's been two days that I can't have access to search the mailing > list. Maybe there is a problem. So please can an

Re: [gmx-users] anisotropic pressure coupling

Shuangxing Dai wrote: Hi all: I was using Parrinello-Rahman for pressure coupling and here is the mdp file: ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps =

Re: [gmx-users] Disk Space

tekle...@ualberta.ca wrote: Dear Chris and Justin, I just read the manual and it stated that I need a .trr file if I want to extend the simulation ( from 5ns -20ns). My question is: For the first 5ns I want to use berendsen thermostat and barostat so that my system will relax faster compa

[gmx-users] anisotropic pressure coupling

Hi all: I was using Parrinello-Rahman for pressure coupling and here is the mdp file: ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 20 ; number of steps for

RE: [gmx-users] the box lengths

Please copy and paste in the commands you are using, and the output. I suspect you have made your box bigger, but it still contains the same number of molecules and you still have pressure coupling on. So when you start the simulation, not surprising that the box compresses again and goes under 2n

RE: [gmx-users] FEP for amino acid mutations.

I would make a new residue in the .rtp file. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 -

Re: [gmx-users] Disk Space

Dear Chris and Justin, I just read the manual and it stated that I need a .trr file if I want to extend the simulation ( from 5ns -20ns). My question is: For the first 5ns I want to use berendsen thermostat and barostat so that my system will relax faster compared to N-H and P-R. Then I wi

[gmx-users] Disk Space

a question like "is this much really enough?" is impossible for me to answer. I suggest that you look at the autocorrelation times of your observables and perhaps (very likely actually) you will realize that you don't need to save nearly as often as you are saving. Also, read the manual abo

Re: [gmx-users] Disk Space

tekle...@ualberta.ca wrote: Dear Chris, Thank you very much! I am planning to set the output control option like this! tinit = 0 nstxout = 2000 nstvout = 0 nstfout = 0 nstlog = 2000 nstenergy = 1000 I want to set

Re: [gmx-users] Disk Space

Dear Chris, Thank you very much! I am planning to set the output control option like this! tinit = 0 nstxout = 2000 nstvout = 0 nstfout = 0 nstlog = 2000 nstenergy = 1000 I want to set the velocity and force option

[gmx-users] Positive Total energy

Hello  I have sent several emails and i am sorry. It is my last attempt to finish this simulation.The molecule i have is C-C-C-C-C-C-O-C-C-O-C-C-O-H or C10H1O3. (ciej molecule) I dont use gromacs librariesthe files i use are attached to the email in which i have descriped step by step the forcef

Re: [gmx-users] Re: moleculetype CU1+ is redefined

You should be careful working with two force fields. They have to be compatible. See http://www.gromacs.org/index.php?title=Documentation/How-tos/Parameterization&highlight=mix. Mensaje citado por afsaneh maleki : > this error is removed. becuse "ion.itp"was included twice in .top and .itp > files

RE: [gmx-users] No Energy Conservation in NVE simulation of liquid mixtures

Yes, but that is done before starting the simulation, so your total energy will still be nicely constant. Berk > Date: Mon, 14 Jun 2010 11:55:18 +0200 > Subject: Re: [gmx-users] No Energy Conservation in NVE simulation of liquid > mixtures > From: tsje...@gmail.com > To: gmx-users@gromacs.org

RE: [gmx-users] No Energy Conservation in NVE simulation of liquid mixtures

Hi, I stopped removing center of mass motion as advised by Tsjerk, but I experience the same problem still. I understand the arguement of subtracting out the momentum, but if this was the sole issue, I should experience the same problem when simulating pure liquids, but I don't. Any more s

Re: [gmx-users] Re: moleculetype CU1+ is redefined

this error is removed. becuse "ion.itp"was included twice in .top and .itp files. i have included two FF into topology file, one for protein and another one for bilayer. Afsaneh On Mon, Jun 14, 2010 at 6:07 PM, Vitaly Chaban wrote: > > When I generate the tpr file with grompp, I get the followi

Re: [gmx-users] ions.itp

afsaneh maleki wrote: Dear justin, thanks for your helpful reply. where Gromacs does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. why in "ions.itp" #ifdef _FF_GROMACS is defended? This corresponds to ffgmx (a deprecated Gromos87 w

[gmx-users] Re: moleculetype CU1+ is redefined

> When I generate the tpr file with grompp, I get the following error. > "Fatal error: moleculetype CU1+ is redefined" > I work on membrane protein that have no atomtype CU1+. why i get error on > CU+? > I have cheked [moleculetypes]  in toplogy file and there  are n't > doplicated. > How to remove

[gmx-users] ions.itp

Dear justin, thanks for your helpful reply. where Gromacs does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. why in "ions.itp" #ifdef _FF_GROMACS is defended? Best wishes, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Re: the box lengths

> First time I meet this problem, > ERROR: One of the box lengths is smaller than twice the cut-off length. > Increase the box size or decrease rlist. > I just followed the advice increase the box size, I tried twice in the > editconf about the box size, actually this box is really large enough f

[gmx-users] question about [ pairs ] and interaction 1-4

Hi there, I mostly use ffamber and sometimes I look in oplsaa to understand how things are implemented in gromacs (4.0.5) I have an example here, where 2 atoms, in a phosphate (see http://en.wikipedia.org/wiki/File:1-hydrogenphosphate-3D-balls.png) in 1-4 interaction that have opposite charges (0

Re: [gmx-users] moleculetype CU1+ is redefined

afsaneh maleki wrote: Hi, When I generate the tpr file with grompp, I get the following error. "Fatal error: moleculetype CU1+ is redefined" I work on membrane protein that have no atomtype CU1+. why i get error on CU+? I have cheked [moleculetypes] in toplogy file and there are n't doplica

Re: [gmx-users] the box lengths

#ZHAO LINA# wrote: From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, June 14, 2010 10:02 PM To: Gromacs Users' List Subject: Re: [gmx-users] the box lengths #ZHAO LINA# wro

RE: [gmx-users] the box lengths

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, June 14, 2010 10:02 PM To: Gromacs Users' List Subject: Re: [gmx-users] the box lengths #ZHAO LINA# wrote: >

[gmx-users] moleculetype CU1+ is redefined

Hi, When I generate the tpr file with grompp, I get the following error. "Fatal error: moleculetype CU1+ is redefined" I work on membrane protein that have no atomtype CU1+. why i get error on CU+? I have cheked [moleculetypes] in toplogy file and there are n't doplicated. How to remove this err

Re: [gmx-users] the box lengths

#ZHAO LINA# wrote: ___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, June 14, 2010 9:33 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the box lengths #ZH

RE: [gmx-users] the box lengths

___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, June 14, 2010 9:33 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the box lengths #ZHAO LINA# wrote: > Hi,

Re: [gmx-users] the box lengths

#ZHAO LINA# wrote: Hi, First time I meet this problem, ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist. I just followed the advice increase the box size, I tried twice in the editconf about the box size, actually this box is re

[gmx-users] the box lengths

Hi, First time I meet this problem, ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist. I just followed the advice increase the box size, I tried twice in the editconf about the box size, actually this box is really large enough for t

[gmx-users] xpm file

Hi everyone, please it's been two days that I can't have access to search the mailing list. Maybe there is a problem. So please can anyone help me? I used the g_covar and got covar.xpm file. My problem is that I can't figure out which application can open the xpm file, so I converted it to .eps f

Re: [gmx-users] position restraint....NEED URGENT HELP

nikhil damle wrote: Hey ! My doubt posted few days back still holds. I am trying to simulate the kinase domain in complex with cyclin. when i keep entire complex either position restrained or flexible, MD runs without any errors. But as soon as i keep cyclin position restrained keeping kina

Re: [gmx-users] Re:gmx-users Digest, Vol 74, Issue 73

fancy2012 wrote: Dear all, Thanks very much for Justin A. Lemkul's explanations! I have got the idea. I have a problem of my mailing list, I can't receive the independent mails from mailing list as before. I can only get the Digest, is there something wrong with my e-mail box? Thanks very muc

[gmx-users] Re:gmx-users Digest, Vol 74, Issue 73

Dear all, Thanks very much for Justin A. Lemkul's explanations! I have got the idea. I have a problem of my mailing list, I can't receive the independent mails from mailing list as before. I can only get the Digest, is there something wrong with my e-mail box? Thanks very much! All the best, fanc

[gmx-users] FEP for amino acid mutations.

Dear GROMACS users, I would like to perform a FEP calculation mutating a residue outside the active site of a protein. I was wondering if I have to create a .itp file for the mutation or it is possible to modify the .rtp file ( adding the state B parameter to the amino acid I would like to change).

Re: [gmx-users] No Energy Conservation in NVE simulation of liquid mixtures

Hey :) Errm, you subtract the overall linear momentum. That affects the kinetic energy, decreasing it, doesn't it? Tsjerk On Mon, Jun 14, 2010 at 10:59 AM, Berk Hess wrote: > Hi, > > Why not? > > Berk > >> Date: Mon, 14 Jun 2010 08:19:30 +0200 >> Subject: Re: [gmx-users] No Energy Conservation

RE: [gmx-users] No Energy Conservation in NVE simulation of liquid mixtures

Hi, Why not? Berk > Date: Mon, 14 Jun 2010 08:19:30 +0200 > Subject: Re: [gmx-users] No Energy Conservation in NVE simulation of liquid > mixtures > From: tsje...@gmail.com > To: gmx-users@gromacs.org > > Hi Godwin, > > I noticed you're removing center of mass motion, which you shouldn't f

[gmx-users] Re: Adding Partial Charges for Small Molecules

Dear Nancy, Just completing what Justin did, see below. On Mon, Jun 14, 2010 at 03:10, wrote: > Nancy wrote: > > Hi All, > > > > I am trying to add partial charges to nicotinamide adenine dinucleotide > > (NAD+), for input to molecular simulations. I have been using the UCSF > > Chimera progra

Re: [gmx-users] soft-core

Hi Well the tutorial in the following website has mentioned about the importance of sc_alpha and sc-power. Also the manual gives you more information. http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial. Regards Sai On Sun, Jun 13, 2010 at 6:56 PM, Justin A. Lemkul wrote: >

Re: [gmx-users] Parallel installation

Hi, you either have to add the directory where mdrun_mpi resides to your path or you have to give mpirun the full path name of mdrun_mpi. You can add the Gromacs executables to your path by the command source /path/to/your/installed/gromacs/bin/GMXRC Or use mpirun -np 12 /path/to/your/installe