[gmx-users] gromacs 3.3.1/4.0 and fftw 3.1.2

Hello, can anybody confirm if fftw-3.1.2 is compatible with gromacs 3.3.1 and gromacs 4.0? A colleague has recently indicated that I must use fftw 2.1.5 for gromacs mpi. However, I have been using fftw-3.1.2 for quite a while now. It compiles fine and my searching today turned up some oth

[gmx-users] Using pull code to simulate slab flow

I am trying to simulate slab flow 5 m/s in the x direction using the afm pull code. I use the following parameters in the pull.ppa file with full periodic boundary conditions. verbose = no runtype = afm ngroups = 1 group_1 = water reference_group = weights_1 = reference_weights = reftype = com_t0

[gmx-users] Is there a way to measure the shortest distance between two groups of atoms?

Hi, all, I was wondering if there is a way to measure the shortest distance between two groups of atoms? g_dist seems to only measure the average distance between the two groups. Your input would be greatly appreciated. Sincerely, Art Roberts

[gmx-users] Is there a way to measure the shortest distance between two groups of atoms?

g_mindist (with or without -pi depending on what you want) Hi, all, I was wondering if there is a way to measure the shortest distance between two groups of atoms? g_dist seems to only measure the average distance between the two groups. Your input would be greatly appreciated. ___

Re: [gmx-users] gromacs 3.3.1/4.0 and fftw 3.1.2

[EMAIL PROTECTED] a écrit : Hello, can anybody confirm if fftw-3.1.2 is compatible with gromacs 3.3.1 and gromacs 4.0? A colleague has recently indicated that I must use fftw 2.1.5 for gromacs mpi. However, I have been using fftw-3.1.2 for quite a while now. It compiles fine and my searchin

[gmx-users] The code : from .pdb to .gro

Hi Could anyone please to direct me the code / the command (pdb2gmx) , which can transfer .pdb file to .gro file? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archi

Re: [gmx-users] gromacs 3.3.1/4.0 and fftw 3.1.2

[EMAIL PROTECTED] wrote: Hello, can anybody confirm if fftw-3.1.2 is compatible with gromacs 3.3.1 and gromacs 4.0? A colleague has recently indicated that I must use fftw 2.1.5 for gromacs mpi. However, I have been using fftw-3.1.2 for quite a while now. It compiles fine and my searching t

Re: [gmx-users] f(x) g(x) h(x)in the user defined potential functions

He, Yang wrote: Hi Mark, Thank you for your reply. From your point of view, I wonder whether you mean I need to write a table based on different interaction types and then change the source code for recognition when running my case in the gromacs. Yes that's what I said. I just have no

Re: [gmx-users] The code : from .pdb to .gro

Chih-Ying Lin wrote: Hi Could anyone please to direct me the code / the command (pdb2gmx) , which can transfer .pdb file to .gro file? It's unlikely you actually need a .gro file for your purpose. pdb2gmx is a tool for making topology files. editconf is the easiest tool for making simple cha

[gmx-users] gromacs 3.3.1/4.0 and fftw 3.1.2

Hi Mark, did you post something on this topic? There is a link indicating that you did but it is broken for some reason. The links above and below work fine. If you wouldn't mind, could you please repost? Thanks, Chris. ___ gmx-users mailing list

[gmx-users] About the example case "A toy peptide in water" and other protein case (CG martini force field )

Dear Sir , I used your CG parameters and gromacs V3.3 to simulate protein aggregation. And my command is : grompp_mpi_d -np 2 -f aggre.mdp -c aggre.gro -p aggre.top -o aggre.trp The error message is : double-checking input for internal consistency... Velocities were taken from a Maxwell distributio

[gmx-users] About the example case "A toy peptide in water" and other protein case (CG martini force field )

Dear Sir , I used your CG parameters and gromacs V3.3 to simulate protein aggregation. And my command is : grompp_mpi_d -np 2 -f aggre.mdp -c aggre.gro -p aggre.top -o aggre.trp The error message is : double-checking input for internal consistency... Velocities were taken from a Maxwell distributio

[gmx-users] About the example case "A toy peptide in water" and other protein case (CG martini force field )

Dear Sir , I used your CG parameters and gromacs V3.3 to simulate protein aggregation. And my command is : grompp_mpi_d -np 2 -f aggre.mdp -c aggre.gro -p aggre.top -o aggre.trp The error message is : double-checking input for internal consistency... Velocities were taken from a Maxwell distributio

[gmx-users] cannot generate .top file

Hi. I seem having some problem in running ./pdb2gmx. Here is the output file. Can you help me in giving me some idea to deal with this? bcsb09s-imac52:bin bcsb09$ pdb2gmx -f 1aml.pdb -p 1aml.top -o 1aml.gro :-) G R O M A C S (-: Getting the Right Output Me

RE: [gmx-users] stochastic dynamics , langevin

> From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: RE: [gmx-users] stochastic dynamics , langevin > Date: Thu, 23 Oct 2008 15:32:02 -0700 > > Along these same lines... > (a)is there an thermostat setting in GROMACS that comes close to the DPD > thermostat as described in (T. Sodd

[gmx-users] table_bonded.xvg

Dear Users In gromacs 4.0, in file force.c in function make_bonded_tables line (1007) sprintf(tabfn + strlen(basefn) - strlen(ftp2ext(efXVG)) - 1,"_%s%d.%s", tabext, i, ftp2ext(efXVG)); produces table_bonded_bonded.xvg instead of table_bonded.xvg Greetings Andrzej Rzepiela

Re: [gmx-users] cannot generate .top file

Kwee Hong wrote: Hi. I seem having some problem in running ./pdb2gmx. Here is the output file. Can you help me in giving me some idea to deal with this? bcsb09s-imac52:bin bcsb09$ pdb2gmx -f 1aml.pdb -p 1aml.top -o 1aml.gro --- Program p

[gmx-users] Warning with L-BFGS minimization

Hi, with l-bfgs minimzation, grompp always reports WARNING 1 [file em.mdp, line unknown]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. even if the mdp gives ; Method for doing electrostatics coulombtype = PME rcoulomb_switch = 0 rcoulomb

Re: [gmx-users] Warning with L-BFGS minimization

Jochen Hub wrote: Hi, with l-bfgs minimzation, grompp always reports WARNING 1 [file em.mdp, line unknown]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. even if the mdp gives ; Method for doing electrostatics coulombtype = PME rcoulomb_switch

[gmx-users] Gromacs 4 SRC RPM?

Is there any eta on when the gromacs-4.0-1.src.rpm is going to show up on: ftp://ftp.gromacs.org/pub/gromacs/rpm Thanks, Mike ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] Warning with L-BFGS minimization

Mark Abraham wrote: > Jochen Hub wrote: >> Hi, >> >> with l-bfgs minimzation, grompp always reports >> >> WARNING 1 [file em.mdp, line unknown]: >> For efficient BFGS minimization, use switch/shift/pme instead of >> cut-off. >> >> even if the mdp gives >> ; Method for doing electrostatics >> coul

Re: [gmx-users] Warning with L-BFGS minimization

Jochen Hub wrote: Mark Abraham wrote: Jochen Hub wrote: Hi, with l-bfgs minimzation, grompp always reports WARNING 1 [file em.mdp, line unknown]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. even if the mdp gives ; Method for doing electrostatics coulombtype

RE: [gmx-users] Warning with L-BFGS minimization

Hi, The problem is you vdwtype setting, not coulombtype. Berk > Date: Fri, 24 Oct 2008 16:08:14 +0200 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Warning with L-BFGS minimization > > Mark Abraham wrote: > > Jochen Hub wrote: > >> Hi, > >> > >> with l-bfgs m

Re: [gmx-users] Gromacs 4 SRC RPM?

On Fri, 2008-10-24 at 09:06 -0500, Mike Hanby wrote: > Is there any eta on when the gromacs-4.0-1.src.rpm is going to show up > on: > > ftp://ftp.gromacs.org/pub/gromacs/rpm You may be able to use the one in Fedora, e.g. http://download.fedora.redhat.com/pub/fedora/linux/updates/9/SRPMS.newkey/g

RE: [gmx-users] Gromacs 4 SRC RPM?

Thanks for the link, I'll take a look at that one. I have to build my own RPM to compile it with Intel compilers and OpenMPI. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jussi Lehtola Sent: Friday, October 24, 2008 9:44 AM To: Discussion list for GROMA

Re: [gmx-users] Warning with L-BFGS minimization

Hi Jochen, It's probably the rvdw cutoff (from readir.c): if (ir->eI == eiLBFGS && (ir->coulombtype==eelCUT || ir->vdwtype==evdwCUT) && ir->rvdw != 0) { warning("For efficient BFGS minimization, use switch/shift/pme instead of cut-off."); } Bummer! Tsjerk On 10/24/08, Jochen Hub <[E

RE: [gmx-users] table_bonded.xvg

Hi, According to me it does not. I never change the default names. But with the default names the table file name option is "table.xvg" and for a tabulated bond table number 0, it correctly opens "table_b0.xvg" Berk > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Date: Fri, 24 Oct 2008

[gmx-users] atoms not part of any of the T-coupling groups

I am a novice at Gromacs (although I used Gromos 20+ years ago!)I have a dimer with two zincs per monomer, and I get the following complaint when running the grompp with pr.dmp, which I assume is referring to the 4 zincs. There are: 6789 OTHER residues There are: 262PROT

Re: [gmx-users] atoms not part of any of the T-coupling groups

garry wrote: I am a novice at Gromacs (although I used Gromos 20+ years ago!)I have a dimer with two zincs per monomer, and I get the following complaint when running the grompp with pr.dmp, which I assume is referring to the 4 zincs. There are: 6789 OTHER residues There are:

[gmx-users] How to assign/make ionion bonds ?

Hi How to assign / make ionion bonds? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)sub

[gmx-users] Does gromacs simulate rotation correctly?

Hi, all, Just curious. Does gromacs simulate rotation correctly? From my observation, it would appear that every object in the simulation both small and large has a similar rotational correlation time, which is not reality. I would expect water for example to have an extremely short ro

Re: [gmx-users] How to assign/make ionion bonds ?

Chih-Ying Lin wrote: Hi How to assign / make ionion bonds? Assign them yourself in the [ bonds ] section of the topology. As for what parameters to assign to such a species, that's up to you; they probably don't exist in the standard force fields within Gromacs... -Justin Thank you Li

Re: [gmx-users] Does gromacs simulate rotation correctly?

On Fri, 24 Oct 2008 10:42:26 -0700 Arthur Roberts <[EMAIL PROTECTED]> wrote: Hi, all, Just curious. Does gromacs simulate rotation correctly? From my observation, it would appear that every object in the simulation both small and large has a similar rotational correlation time, which is n

[gmx-users] The structure property

Hi >From the following tutorial, the protein pdb file is downloaded from the Protein Data Bank. Before running the MD simulation, we have to make sure the structure property. I have some questions about this tutorials. http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ 1. Make sure that there are

[gmx-users] atom name in pdb converted by editconf (gmx4)

Hi, I found that when the output format from editconf (gmx4) is PDB, atom name like H5'1 will be changed to 1H5'. For other four-character atom name like ABCD, editconf works properly. example: editconf -f a.pdb -o b.pdb = a.pdb == ATOM 1 PDT 1 -1.84

Re: [gmx-users] The structure property

Chih-Ying Lin wrote: Hi From the following tutorial, the protein pdb file is downloaded from the Protein Data Bank. Before running the MD simulation, we have to make sure the structure property. I have some questions about this tutorials. http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/

Re: [gmx-users] atoms not part of any of the T-coupling groups

Garry, I believe you are trying to not temperature couple the 4 zincs. To do this put the 4 zincs in one group and include that group in the listing of tc_grps and then correspondingly assign tau_t. tau_t=0 means no temperature coupling, but I think you will also need to give a temperature for the

Re: [gmx-users] atoms not part of any of the T-coupling groups

Wouldn't it be better to couple the Protein and Zn2+ together (i.e., index group Protein_Zn2+)? Coupling ions separately often leads to weird behavior/explosions when they're free in the solvent. I've never dealt with proteins that have ions bound, so I'm curious to see what everyone else thin

Re: [gmx-users] The structure property

Hi Lin, Justin is right on all points. The first is indeed a check you should always perform, but in this case (1LW9), there are no missing residues/atoms. The point is that one should be aware that there could. The same thing goes with the hint for the histidines. I could have not written you sho

RE: [gmx-users] f(x) g(x) h(x)in the user defined potential functions

Hi Mark, Thank you for your reply. From your point of view, I wonder whether you mean I need to write a table based on different interaction types and then change the source code for recognition when running my case in the gromacs .I just have no idea about that .Can you give me further sugg