Re: [gmx-users] Re: grompp: Atoms in the .top are not

Hi, Putting ions as individual molecule is quite a standard practice. Looking at ions.itp in the top directory. I added ions there with new forcefield preprocessor directives. Most gromacs users except you will get a low mark, I reckon. I tried your way in the previous and just now. It works

Re: [gmx-users] Re: gmx-users Digest, Vol 25, Issue 5

Hi, On May 4, 2006, at 4:19 AM, gil claudio wrote: Thanks for the help, Erik and David. Does this mean that when invoking rb dihedrals, the real equation being used is RB(phi) = C0 - C1 cos(phi) + C2 cos^2(phi) - C3 cos^3(phi) + C4 cos^4(phi) - C5 cos^5(phi) Yes, if you convert it to bioch

Re: [gmx-users] Compressibility in NpT: What value to input?

Hi! I've seen it on the manual too. But one doubt arise: Wouldn't that value affect some other pressure dependent properties when calculated, like exactly the liquid compressibility" Thanks a lot in advance! Jones On 5/3/06, Erik Lindahl <[EMAIL PROTECTED]> wrote: Hi,Just use the water value for

Re: [gmx-users] Re: Benching against different compilers - Help needed

Hi. Bad news. :( I was compiling it in portland with the -tp=k8-64 -fastsse -Mipa=fast -Mipa=inline. Oficially, as in some AMD documentation, the first two are mandatory. So, I first tried without the -Mipa ones, and it yelded me the same results as with them. Then, I tried to remove the -fastss

[gmx-users] Re: gmx-users Digest, Vol 25, Issue 5

Thanks for the help, Erik and David. Does this mean that when invoking rb dihedrals, the real equation being used is RB(phi) = C0 - C1 cos(phi) + C2 cos^2(phi) - C3 cos^3(phi) + C4 cos^4(phi) - C5 cos^5(phi) It might be good to mention this convention in the manual. Message: 3 Date: Tue, 2 Ma

Re: [gmx-users] Re: grompp: Atoms in the .top are not

numbered consecutively References: <[EMAIL PROTECTED]> In-Reply-To: <[EMAIL PROTECTED]> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.7 X-Authenticated-User: densign X-Originating-IP: 171.65.103.75 Regardi

RE: [gmx-users] A question about general MD procedure

Title: Message Can't really help you directly (and since noone else has chipped in with something thought I'd at least give you some direction), but with majority of things like this two things you can do to get things going: read papers (and this emailing list) dealing with "similar things"

Re: [gmx-users] Re: grompp: Atoms in the .top are not numbered consecutively

D. Ensign wrote: I'm having a lovely time with my old pal grompp, except for the grumpiness after replacing eight water molecules with ions in my system and discovering -- to my astonishment -- the following message: "Atoms in the .top are not numbered consecutively from 1" Well, this is intere

Re: [gmx-users] Re: grompp: Atoms in the .top are not numbered consecutively

Try this: 1. Paste this at the place of my_ions.itp to replace it. [ moleculetype ] NA+ 1 [ atoms ] 1 amber99_31 1 NA+ NA+ 1 122.99000 [ moleculetype ] CL- 1 [ atoms ] 1 amber99_30 1 CL- CL- 1 -1

[gmx-users] Re: grompp: Atoms in the .top are not numbered consecutively

> > > I'm having a lovely time with my old pal grompp, except for the > > > grumpiness after > > > replacing eight water molecules with ions in my system and discovering -- > > > to my > > > astonishment -- the following message: > > > > > > "Atoms in the .top are not numbered consecutively from

Re: [gmx-users] Compressibility in NpT: What value to input?

Hi, Just use the water value for any liquid system (5e-5 or so). As the manual explains, it only affects the coupling time, not the equilibrium pressure. Cheers, Erik On May 3, 2006, at 8:54 PM, Jones de Andrade wrote: Hi all. Ok, this may sound like a stupid question, since the equati

Re: [gmx-users] lipid.itp LJ-1,4 values involving water

Hi, They were almost certainly auto-generated from the standard parameters. Cheers, Erik On May 3, 2006, at 8:44 PM, [EMAIL PROTECTED] wrote: Does anyone know why lipid.itp contains [pairtypes] LJ-1,4 values including lipid atoms and OW or HW? I can understand their inclusion in [nonbond_

[gmx-users] energy minimization in vacuum

Dear Gmx-users, I have questions about energy minimization in vacuum. Since there are two force fields available, G43a1 and G43b1, I should use G43b1 for energy minimization in vacuum? What are the major difference between these two force fields? In one previous paper (Amadei et al, 1999), a laye

Re: [gmx-users] graph edges bug?

James Rustad wrote: Hi List, I am running into a "max graph edges exceeded" problem with gromacs 3.3. I can run my molecule fine with "pbc = no" but when I change it to "pbc = xyz" I get - Program mdrun_d, VERSION 3.3 Source code file: m

[gmx-users] Re: grompp: Atoms in the .top are not numbered consecutively

from 1 References: <[EMAIL PROTECTED]> In-Reply-To: <[EMAIL PROTECTED]> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.7 X-Authenticated-User: densign X-Originating-IP: 171.65.103.75 > > I'm having a lovely

[gmx-users] graph edges bug?

Hi List, I am running into a "max graph edges exceeded" problem with gromacs 3.3. I can run my molecule fine with "pbc = no" but when I change it to "pbc = xyz" I get - Program mdrun_d, VERSION 3.3 Source code file: mshift.c, line: 95 Fa

[gmx-users] Compressibility in NpT: What value to input?

Hi all. Ok, this may sound like a stupid question, since the equations of the barostats clearly states the compressibility constant in it. But, in other programas I used to do NpT (usually with Nosè-Hoover) simulations, like DL_Poly and MDynaMix, I never had to input this parameter. Only referen

[gmx-users] lipid.itp LJ-1,4 values involving water

Does anyone know why lipid.itp contains [pairtypes] LJ-1,4 values including lipid atoms and OW or HW? I can understand their inclusion in [nonbond_params], but it seems as if this would never be required in [pairtypes]. *** In case anyone else is trying to merge lipid.itp and OPLSAA, here is what

Re: RE : RE : [gmx-users] segmentation fault in mdrun when using PME

Hi Diane, On May 3, 2006, at 5:45 PM, Diane Fournier wrote: It seems that in my case this is a bug (see Bugzilla, bug # 74) related to using the Intel Math Kernel Library (MKL) v. 8.0.1 for Fourier transforms. The team managing the Altix are trying different FFT libraries. Eric Lindahl sa

RE : RE : [gmx-users] segmentation fault in mdrun when using PME

It seems that in my case this is a bug (see Bugzilla, bug # 74) related to using the Intel Math Kernel Library (MKL) v. 8.0.1 for Fourier transforms. The team managing the Altix are trying different FFT libraries. Eric Lindahl says that using a FFT library that is not optimized for Itanium 2 sh

Re: [gmx-users] Re: Benching against different compilers - Help needed

Jones de Andrade wrote: Hi again. Well, here we go: On 4/30/06, David van der Spoel <[EMAIL PROTECTED]> wrote: Jones de Andrade wrote: > Up to now, I could finally compile it with Portland, in both single and > double precision version. But, on the other hand, while the single > precision wor

[gmx-users] Re: Benching against different compilers - Help needed

Hi again. Well, here we go: On 4/30/06, David van der Spoel <[EMAIL PROTECTED]> wrote: Jones de Andrade wrote: > Up to now, I could finally compile it with Portland, in both single and > double precision version. But, on the other hand, while the single > precision works properly, the double p

Re: [gmx-users] atomtype

Hi!I'm sorry, I realize I didn't mention in my first reply that you should download the new version of ffgmx modified for describing lipids to be used with the popc.itp topology file, you can find it at this link: http://www.gromacs.org/topologies/force_fields.php"Invalid order for directive atomty

[gmx-users] atomtype

Hi,everyone, I have tried to use popc.pdb that the coordinates are from Tieleman's web to insert a protein.when i use ffgmx.itp , there is fetal error: atomtype LC3 not found. i downloaded ffgmx_lipid but i have a problem: fetal error: invalid order for directive atomtypes file .share\top\...

Re: [gmx-users] Info on the "Ellipticity at 222 nm" provided by g_helix

Afonso Duarte wrote: Dear All, I am a newbie using GROMACS and I am just going throu my first sims. I have one question regarding the output of g_helix. Using this command get a value for the "Ellipticity at 222 nm according to Hirst and Brooks" however this value is in nm (per time frame) an

Re: [gmx-users] cross compiling gromacs

ganapathy senthilkumar wrote: dear gromacs users, I tried to cross-compile gromacs for powerpc on an intel x86 machine. i set the configure options as export CPPFLAGS=-I/mnt/usr/local/include export LDFLAGS=-L/mnt/usr/local/lib =>i had mounted another root file system(simulated) ont

[gmx-users] Info on the "Ellipticity at 222 nm" provided by g_helix

Dear All, I am a newbie using GROMACS and I am just going throu my first sims. I have one question regarding the output of g_helix. Using this command get a value for the "Ellipticity at 222 nm according to Hirst and Brooks" however this value is in nm (per time frame) and for 100% a-helices it sh

[gmx-users] cross compiling gromacs

dear gromacs users,I tried to cross-compile gromacs for powerpc on an intel x86   machine. i set the configure options as export CPPFLAGS=-I/mnt/usr/local/include export LDFLAGS=-L/mnt/usr/local/lib =>i had mounted another root file system(simulated) onto mnt. i ran the configure script w

[gmx-users] A question about general MD procedure

Hi,dear GMX group and other users: First of all, I wanna thank Yang Ye, David, Mark and others for your instant replies to most our online questions. I am a new user of gromacs(version 3.3). I want to do carbon nanotube MD (to obtain the relationship between axial compressive force and the tube's c

RE: [gmx-users] Highest possible temperature in NPT?

From: [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] Highest possible temperature in NPT? Date: Tue, 02 May 2006 16:39:57 +0200 (MEST) Dear community, I am trying to perform some wild REMD tests, and see the effect of very high