[gmx-users] Water model => amber port to gromacs

Hi Water model => amber port to gromacs The two steps are shown on the archive. 1. #include ffamber_tip*pin the .top file 2. include an #ifdef_FF_AMBER statement in tip*p.itp Should I also #include ffamber99.tip in the .top file? Thank you Lin __

Re: [gmx-users] How does GROAMCS handle PME with non-zero charge

Himanshu Khandelia wrote: Hi, How does GROMACS handle PME calculations if the system has non-zero charge. Does it automatically apply a neutralizing charge density ? A little searching with Google would have found you the answers... http://www.gromacs.org/pipermail/gmx-users/2004-May/010509.

Re: [gmx-users] how much ns

vivek sharma wrote: Hi Marc, Can you give an approximate time estimate for too short and too long time of simulation, if I am running simulation for protein in water to see the conformational changes ? It varies wildly. Some biochemical processes might happen inside a nanosecond. Others take

[gmx-users] How does GROAMCS handle PME with non-zero charge

Hi, How does GROMACS handle PME calculations if the system has non-zero charge. Does it automatically apply a neutralizing charge density ? Thank you -Himanshu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinf

Re: [gmx-users] rmsd on homologous protein structure

Hi, For individual structures, you can use g_confrms. If you want a trajectory you can download do_multiprot from the user contributions section, and follow the instructions there. Note that multiprot aligns based on the structure only (no sequence information). Ran. Tatsiana Kirys wrote: > Hi,

Re: [gmx-users] how much ns

Hi Marc, Can you give an approximate time estimate for too short and too long time of simulation, if I am running simulation for protein in water to see the conformational changes ? With Thanks, Vivek 2008/11/6 Marc F. Lensink <[EMAIL PROTECTED]> > On Thu, Nov 06, 2008 at 03:08:53PM +0530, Bhawa

[gmx-users] missing of methyl at N-terminal

hello everyone, for doing peptide with usual amino acid simulation. i m bringing my *.pdb file from insightII as i dont know any other tool or software from where i can get any pdb file (model peptide-Eg. Ac-Ala-Ala-Ala-Ala-NHMe).But when i put my pdb file in gromacs by using pdb2gmx. it give err

Re: [gmx-users] mdp file

He, Yang wrote: Hi all users, When I use the command "mdrun -tablep table.xvg " to run my model in gromacs, it always shows that: starting mdrun 'DNA in water' 1 steps, 20.0 ps. This is orders of magnitude too short to expect a large conformational change to happen. Think nanosecon

Re: [gmx-users] rmsd on homologous protein structure

Tatsiana Kirys wrote: Hi, i want to calculate rmsd on homologous protein structures that have different residue numbers. As far as i understood g_rms gives only rmsd of the same structure in different configurations, but it doesn't fit homologous protein structures? Yep. In Option -f2 can

Re: [gmx-users] running a simulation without production

Zuzana Benkova wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Zuzana Benkova Sent: Tuesday, November 04, 2008 3:11 PM To: 'Discussion list for GROMACS users' Subject: RE: [gmx-users] running a simulation without production Dear Mark, Thank you

Re: [gmx-users] way to cap C-terminal as CONH2

Justin A. Lemkul wrote: sarbani chattopadhyay wrote: Hi everyone, I want to know is there any way to add Amide cap at the C terminal end of the protein using gromacs. Using "pdb2gmx -ter" doesnot give CONH2 as one of the options. The -NH2 group must be present in th

[gmx-users] rmsd on homologous protein structure

Hi, i want to calculate rmsd on homologous protein structures that have different residue numbers. As far as i understood g_rms gives only rmsd of the same structure in different configurations, but it doesn't fit homologous protein structures? In Option -f2 can i provide a trajectory of a ho

[gmx-users] Test Set for Gromacs 4?

Is there a test set available for Gromacs 4? I looked here and found 3.3.2 and 3.3.3: ftp://ftp.gromacs.org/pub/tests/ Thanks, Mike ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the a

Re: [gmx-users] Re: .xtc file is incomplete

xianghong qi wrote: haha, thanks for your explanation. Justin. So you think I should stop my simulation. If you are trying to re-run the first simulation, it may work just fine. If you are using the .tpr file generated from the incomplete .trr, then it may work as well, just be careful tha

Re: [gmx-users] weird behavior of genion in gromacs4

Serena Leone wrote: Hi all I'm trying for the first time to use the opls aa in gromacs4. When I tried to use genion (my peptide has charge +7) I had the following problem: genion -s H1_em.tpr -conc 0.1 -neutral -nname opls_401 -pname opls_407 -p H1_opls.top -o H1_ions.gro You should pr

[gmx-users] weird behavior of genion in gromacs4

Hi all I'm trying for the first time to use the opls aa in gromacs4. When I tried to use genion (my peptide has charge +7) I had the following problem: genion -s H1_em.tpr -conc 0.1 -neutral -nname opls_401 -pname opls_407 -p H1_opls.top -o H1_ions.gro [...] Reading file H1_em.tpr, VERSION

Re: [gmx-users] Re: .xtc file is incomplete

haha, thanks for your explanation. Justin. So you think I should stop my simulation. I am trying to test whether my result is reasonable. Thanks anyway. -Xianghong Qi On Thu, Nov 6, 2008 at 3:03 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > xianghong qi wrote: > >> Hello, everyone: >> >>

Re: [gmx-users] Re: .xtc file is incomplete

xianghong qi wrote: Hello, everyone: when I run simulation, I got incomplete .xtc file, incomplete .trr file, but I have a complete log file. Then I use this incomplete to create input file for mdrun, I got the reasonable size of .tpr file. I wouldn't trust that .tpr file to contain what y

[gmx-users] Re: .xtc file is incomplete

Hello, everyone: when I run simulation, I got incomplete .xtc file, incomplete .trr file, but I have a complete log file. Then I use this incomplete to create input file for mdrun, I got the reasonable size of .tpr file. I am confused what happed there. Does anyone has some idea about this? actua

RE: [gmx-users] problem with openmpi and gromacs4.0

Hi, Older tpr versions are compatible with 4.0. For large systems making a new tpr file with the 4.0 grompp will inprove the performance. Berk From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] problem with openmpi and gromacs4.0 Date: Thu, 6 Nov 2008 17:56:28 +0100

[gmx-users] Mean squared displacement for fast moving particles

Hi all ! I want to calculate Mean squared displacement of fast moving particles from a gromacs trajectory. The way I will define fast moving particles is choice based, lets say particles which have possess velocities 2 standard deviations above the mean velocities at a given temperature. Does

Re: [gmx-users] Interactions between tow chains of a protein

Polavarapu, Abhigna wrote: Hi All, I am abhigna. I wanted to simulate a protein which binds to Copper. Copper interacts with amino acids of Chain A and B of the Dimeric protein. When I convert the pdb file to topology file this is how it defines with A and B with protein and C and D w

[gmx-users] mdp file

Hi all users, When I use the command "mdrun -tablep table.xvg " to run my model in gromacs, it always shows that: starting mdrun 'DNA in water' 1 steps, 20.0 ps. Warning: 1-4 interaction between 11 and 19 at distance 1.437 which is larger than the 1-4 table size 1.000 nm These are ign

Re: [gmx-users] problem with openmpi and gromacs4.0

On Nov 6, 2008, at 15:04 , hui sun wrote: Dear all, Recently, we installed the gromacs4.0 with openmpi parallel program. When we started a simulation with np=1, the simulation was finished normally. But when the same tpr file was run with np=n (n>1), I obtained the following error messag

Re: [gmx-users] RE: vsite problem in gromacs 4.0

On Nov 6, 2008, at 14:48 , Berk Hess wrote: Hi, I fixed the virtual site charge group issue in mdrun for 4.0.1. Now vsite aromatics will run fine. But there is still an issue in pdb2gmx for some proteins when selecting the OPLS force field. I hope we can fix this for 4.0.1. Is it something

RE: [gmx-users] RE: vsite problem in gromacs 4.0

Ah, sorry, the email I replied to does not contain the whole history. There are only issues with vsite aromatics in Gromacs 4.0 (and they will cause a fatal error or segv, no incorrect results). All other applications of virtual sites are unaffected. Berk From: [EMAIL PROTECTED] To: gmx-users@g

Re: [gmx-users] RE: vsite problem in gromacs 4.0

On Nov 6, 2008, at 17:45 , Daniel Larsson wrote: On Nov 6, 2008, at 14:48 , Berk Hess wrote: Hi, I fixed the virtual site charge group issue in mdrun for 4.0.1. Now vsite aromatics will run fine. But there is still an issue in pdb2gmx for some proteins when selecting the OPLS force field.

RE: [gmx-users] problem with openmpi and gromacs4.0

I would suggest that you test OpenMPI first using a simple hello world on 32 processors to see if it can run successfully: $ mkdir -p ~/jobs/helloworld && cd ~/jobs/helloworld $ vi ./helloworld-mpi.c /*-code*/ #include #include int main

[gmx-users] Interactions between tow chains of a protein

Hi All, I am abhigna. I wanted to simulate a protein which binds to Copper. Copper interacts with amino acids of Chain A and B of the Dimeric protein. When I convert the pdb file to topology file this is how it defines with A and B with protein and C and D with Copper. So I need to define

Re: [gmx-users] way to cap C-terminal as CONH2

sarbani chattopadhyay wrote: Hi everyone, I want to know is there any way to add Amide cap at the C terminal end of the protein using gromacs. Using "pdb2gmx -ter" doesnot give CONH2 as one of the options. The -NH2 group must be present in the .pdb file, and you choo

RE: [gmx-users] running a simulation without production

-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Zuzana Benkova Sent: Tuesday, November 04, 2008 3:11 PM To: 'Discussion list for GROMACS users' Subject: RE: [gmx-users] running a simulation without production Dear Mark, Thank you very much for valuable

[gmx-users] way to cap C-terminal as CONH2

 Hi everyone, I want to know is there any way to add Amide cap at the C terminal end of the protein using gromacs. Using "pdb2gmx -ter" doesnot give CONH2 as one of the options. Any suggestion is welcome. Thanks in advance Sarbani _

RE: [gmx-users] Problem with setting vsite=aromatics on OPLSAA

Hi, I fixed the bug in pdb2gmx. This bug would cause a segv with vsite aromatics in larger proteins. I also fixed the issue in mdrun with vsite aromatics. So now vsite aromatics will be fully functional in 4.0.1. Berk From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: RE: [gmx-users]

[gmx-users] problem with openmpi and gromacs4.0

Dear all, Recently, we installed the gromacs4.0 with openmpi parallel program. When we started a simulation with np=1, the simulation was finished normally. But when the same tpr file was run with np=n (n>1), I obtained the following error message: MPI_ABORT invoked on rank 0 in co

Re: [gmx-users] About the gromacs 4.0 manual and parallel running

2. How to run a parallel simulation with Gromacs 4.0? Are there any special tips for a optimized parallel run? I've tried a set of runnings but found the accelerations are not good enough as I expected. I do something like this (for 8 CPUs): $ grompp -c system.gro -p topology.top -f somethi

RE: [gmx-users] RE: vsite problem in gromacs 4.0

Hi, I fixed the virtual site charge group issue in mdrun for 4.0.1. Now vsite aromatics will run fine. But there is still an issue in pdb2gmx for some proteins when selecting the OPLS force field. I hope we can fix this for 4.0.1. Berk > Date: Tue, 4 Nov 2008 11:32:46 -0500 > From: [EMAIL PROT

[gmx-users] About the gromacs 4.0 manual and parallel running

Hi, I'm using the newly published Gromacs 4.0 package these days. Compared with the prior versions, this version seems to have been improved a lot. From the ftp site, I've downloaded a manual for this version. But this manual seems to be incompleted, which can be revealed in the descriptions of

Re: Re: Re: [gmx-users] can't find "distclean"

 Hi Martin, Thank you for the insight. This is actually true. Since I had used binary package to install gromacs , the source and the configuration directories are not given. Then I am left with no other option but to load gromacs again. Thanking you, Sarbani On Thu, 06 Nov 200

Re: [gmx-users] Compiling Gromacs 4 using Intel Compilers

Mike Hanby wrote: Howdy, I'd like to use "--with-external-blas --with-external-lapack --with-fft=fftw3 --with-gsl" and the Intel v10.1 compilers on a Linux (Centos 5 x86_64) system. My question, do I first need to compile blas, lapack, fftw3 and gsl using the Intel compilers, or will the librar

Re: [gmx-users] how much ns-one more question

On Thu, Nov 06, 2008 at 04:13:04PM +0530, Bhawana Gupta wrote: > thanks for reply. > but sir, when i start it with 1ns md simulation,my peptide doesnot get > stable because it was moving in zigzag like motion. > so should i go for 5 ns or not. > which ns means (1ns or 2ns...20ns) is better so t

Re: Re: [gmx-users] can't find "distclean"

Am Donnerstag, den 06.11.2008, 10:23 + schrieb sarbani chattopadhyay: > Does this mean thai I can't recompile gromacs because I had used a > binary package for > installing gromacs. > Isn't there any way in which I can compile gromacs, without having to > install it again? If you install a

[gmx-users] how much ns-one more question

thanks for reply. but sir, when i start it with 1ns md simulation,my peptide doesnot get stable because it was moving in zigzag like motion. so should i go for 5 ns or not. which ns means (1ns or 2ns...20ns) is better so that i can get good results. with regards Bhawana ___

Re: Re: [gmx-users] can't find "distclean"

 Does this mean thai I can't recompile gromacs because I had used a binary package for installing gromacs. Isn't there any way in which I can compile gromacs, without having to install it again? On Thu, 06 Nov 2008 Martin Höfling wrote : >You're probably not in a source directory. > >As you

RE: [gmx-users] trjconv -f .cpt -s .tpr -o .gro

Hi, This is a bug caused by last minute additions of some stuff to the checkpoint file. I have fixed it for 4.0.1. Berk > Date: Wed, 5 Nov 2008 22:24:15 -0500 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] trjconv -f .cpt -s .tpr -o .gro > > Hello, > > has anybo

RE: [gmx-users] Error with editconf 4.0

Hi, That is another small bug in the 4.0 release. I had already fixed this for 4.0.1. Berk > Date: Wed, 5 Nov 2008 17:19:34 -0500 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] Error with editconf 4.0 > > > Hi all, > > I was trying to dump out a .gro file

Re: [gmx-users] problem

Hi, > i m just getting started to Gromacs > but i have included porse.itp in my topology file. > i m not getting that what does this mean Here you can find some great information: http://www.gromacs.org/documentation/reference/online/speptide.html#posres There are great tutorials and sites out t

Re: [gmx-users] can't find "distclean"

You're probably not in a source directory. As you mentioned - you need an mpi-enabled version (linked vs your installed MPI library). If you're unexperienced in compiling, check first if there are binary packages (with mpi) for OS X. If not, here the roughly sketched steps: - obtain the source (

Re: [gmx-users] how much ns

On Thu, Nov 06, 2008 at 03:08:53PM +0530, Bhawana Gupta wrote: > hi, > > i want to ask that how we can know that how much ns(1 ns or 2 ns.20 ns), > we can run on our system which doing md simulations. > Means how we cme to know that if we go for 5 ns, then our system will not > hang or crash

[gmx-users] problem

Sir, thankyou for reply i m just getting started to Gromacs but i have included porse.itp in my topology file. i m not getting that what does this mean that it is not present in the current directory. whether i had to make porse.itp file and then save in my current directory. Also tell me what is

[gmx-users] how much ns

hi, i want to ask that how we can know that how much ns(1 ns or 2 ns.20 ns), we can run on our system which doing md simulations. Means how we cme to know that if we go for 5 ns, then our system will not hang or crash out. Please help me. with regards Bhawana ___

Re: [gmx-users] problem

Am Donnerstag, den 06.11.2008, 09:58 +0530 schrieb Bhawana Gupta: well, maybe as a first step, you should choose a more informative error description as "problem" as subject. :-) > i m sending this mail regarding the problem which i get after using > grompp command for em.mdp > ERROR is [file

[gmx-users] can't find "distclean"

  Hi, I am facing a peculiar problem and may sound stupid, but I need help. We have a 10.4.1. Mac Os X machine with 2 dual core processors. I had downloaded gromacs 3.3.2 and installed it in this computer using "installer". It added the "gromacs " directory into " "/usr/loca/" directory. I

Re: [gmx-users] Repeating the simulation

Hi QIU YI HUAN, Radius of gyration is a configuration dependent property. You need statistics for that, so you should have more simulations. Jochens example of the rdf is one where the statistics comes from the number of molecules in your system (quite a number for water, versus one self-assembled