[gmx-users] how to differentiate crystal water and explicit waters in gromacs ???

Hi, I am new to GROMACS and I am trying to perform a MD run in PBC condition with water as solvent. I want to keep the crystal water molecules different from explicit waters, I believe this helps me in analysis of crystal waters. Can someone help me wit this ??? Thanking you. regards,

Re: [gmx-users] unit of surface tension, KJ/mol?

Thanks Mark for the hints. I am using a pre equilibrated box for both runs. Can you again explain how Can I interpret this from fluctuations from two runs? Below is the resutls from two versions: Thanks! 4.0.7 Statistics over 733801 steps [ 0. thru 1467.6001 ps ], 1 data sets All averages are

Re: [gmx-users] unit of surface tension, KJ/mol?

On 23/03/11, Elisabeth wrote: > > > On 22 March 2011 22:46, Justin A. Lemkul wrote: > > > > > > > > > > > > > Elisabeth wrote: > > > > > > > > > > > > > > > > > > > > > > On 22 March 2011 22:31, Justin A. Lemkul > > > wrote: > > > > > > > > > > > > >

Re: [gmx-users] unit of surface tension, KJ/mol?

On 22 March 2011 22:46, Justin A. Lemkul wrote: > > > Elisabeth wrote: > > >> >> On 22 March 2011 22:31, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Elisabeth wrote: >> >>Hello, >> I did two simulations on the same system using versions 4.0.7 >>and 4.5.3. It

Re: [gmx-users] unit of surface tension, KJ/mol?

Elisabeth wrote: On 22 March 2011 22:31, Justin A. Lemkul > wrote: Elisabeth wrote: Hello, I did two simulations on the same system using versions 4.0.7 and 4.5.3. It seems like the unit of surface tension is not the same in th

Re: [gmx-users] unit of surface tension, KJ/mol?

On 22 March 2011 22:31, Justin A. Lemkul wrote: > > > Elisabeth wrote: > >> Hello, >> I did two simulations on the same system using versions 4.0.7 and 4.5.3. >> It seems like the unit of surface tension is not the same in these versions >> because I am getting ~250 KJ/mol an in 4.0.7 and ~ 5000

Re: [gmx-users] unit of surface tension, KJ/mol?

Elisabeth wrote: Hello, I did two simulations on the same system using versions 4.0.7 and 4.5.3. It seems like the unit of surface tension is not the same in these versions because I am getting ~250 KJ/mol an in 4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can be converted into bar nm? Can

[gmx-users] unit of surface tension, KJ/mol?

Hello, I did two simulations on the same system using versions 4.0.7 and 4.5.3. It seems like the unit of surface tension is not the same in these versions because I am getting ~250 KJ/mol an in 4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can be converted into bar nm? Can anyone help please. Tha

Re: [gmx-users] Parameterization of a molecule containing a radical (oxygen)

Simone Cirri wrote: Hi all, I have a question regarding a new parameterization: actually, I'm wondering whether or not it is possible to do it. The molecule is tempol; you cand find its PubChem entry here http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994&loc=ec_rcs

Re: [gmx-users] Alcohol Dehydrogenase MD simulation....Reg

On 23/03/2011 4:38 AM, Kishore wrote: Dear All, I had been in the look out for someone who has a reasonable amount of expertise in dealing with the MD simulation of an Alcohol Dehydrogenase. I have a problem dealing with the NADPH. I was unable to maintain the planarity of the carboxamide of

Re: [gmx-users] install problems cygwin

On 23/03/2011 4:10 AM, vijaya subramanian wrote: Hi I tried doing it from my home directory. It didn't work. Also gcc hello.c and g77 hello.f don't produce executables, though both seem to run-not a.out file is created. The Cygwin linker package is not installed by default - you need the "b

Re: [gmx-users] Tables - two non-bonded interactions

Hello I think the easiest way to do this is to use multiple tables. Look at: http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials There are some details there. ciao Gareth 2011/3/22 Vinícius Contessoto : > hello! > I trying to simulate a protein with C-alpha model (my protein hav

[gmx-users] Tables - two non-bonded interactions

hello! I trying to simulate a protein with C-alpha model (my protein have only alpha-carbons) . I need two different interatomic interactions. 1 - Some interactions in a specific alpha-carbons, using a Lennard Jones 10 -12 potential (i'm determining the pairs in my topology file). 2 - All carbon

Re: [gmx-users] Hydroixde Ion

SHIVANGI NANGIA wrote: Hi, Thanks so much for the prompt help. Yes, I did realize that methanol as solvent was not updated in the .top file. I had to fix the .top file manually. When I add ions using genion I replace methanol. As a test I tried setting up the whole system with the change

Re: Re: Re: Re: [gmx-users] Hydroixde Ion

Hi, Thanks so much for the prompt help. Yes, I did realize that methanol as solvent was not updated in the .top file. I had to fix the .top file manually. When I add ions using genion I replace methanol. As a test I tried setting up the whole system with the change that instead of 8 hydroxide i

Re: [gmx-users] Hydroixde Ion

SHIVANGI NANGIA wrote: Hi again, I have the following: I have not changed anything in ffG53a6.atp and .rtp As suggested by gmx users, I have the following in the ions,itp file [ moleculetype ] ; molname nrexcl OH1 [ atoms ] ; id at type res nr residu name at name cg nr charge

Re: Re: Re: [gmx-users] Hydroixde Ion

Hi again, I have the following: I have not changed anything in ffG53a6.atp and .rtp As suggested by gmx users, I have the following in the ions,itp file [ moleculetype ] ; molname nrexcl OH1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 OH 1 OHOH 1

Re: [gmx-users] Various web issues

Thanks for the fix! -Justin Rossen Apostolov wrote: Hi again, On 3/22/11 6:57 PM, Justin A. Lemkul wrote: I posted this a few days ago, but the problem persists - the "search" feature on the Gromacs site either returns an error or completely nonsensical content. Can someone please look int

Re: [gmx-users] Various web issues

Hi again, On 3/22/11 6:57 PM, Justin A. Lemkul wrote: I posted this a few days ago, but the problem persists - the "search" feature on the Gromacs site either returns an error or completely nonsensical content. Can someone please look into why this is so? Manual navigation is very tedious.

Re: [gmx-users] Various web issues

Hi Justin, On 3/22/11 6:57 PM, Justin A. Lemkul wrote: Hi, I posted this a few days ago, but the problem persists - the "search" feature on the Gromacs site either returns an error or completely nonsensical content. Can someone please look into why this is so? Manual navigation is very te

[gmx-users] Various web issues

Hi, I posted this a few days ago, but the problem persists - the "search" feature on the Gromacs site either returns an error or completely nonsensical content. Can someone please look into why this is so? Manual navigation is very tedious. A couple of other things: 1. manual.gromacs.org

Re: [gmx-users] Hydroixde Ion

SHIVANGI NANGIA wrote: Hello, Thanks a lot for the suggestion. I think I made some progress but I am not there yet. I added the following in the ions.itp file [ moleculetype ] ; molname nrexcl OH1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 OH 1 OHOH

[gmx-users] Alcohol Dehydrogenase MD simulation....Reg

Dear All, I had been in the look out for someone who has a reasonable amount of expertise in dealing with the MD simulation of an Alcohol Dehydrogenase. I have a problem dealing with the NADPH. I was unable to maintain the planarity of the carboxamide of the nicotinamide moiety in the simulation a

Re: Re: [gmx-users] Hydroixde Ion

Hello, Thanks a lot for the suggestion. I think I made some progress but I am not there yet. I added the following in the ions.itp file [ moleculetype ] ; molname nrexcl OH1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 OH 1 OHOH 1 0 1 OW 1 OWOW 1 -

RE: [gmx-users] install problems cygwin

Hi I tried doing it from my home directory. It didn't work. Also gcc hello.c and g77 hello.f don't produce executables, though both seem to run-not a.out file is created. Vijaya > From: rol...@utk.edu > Date: Tue, 22 Mar 2011 12:51:45 -0400 > Subject: Re: [gmx-users] install problems cygwin >

Re: [gmx-users] New maintenance release: gromacs-4.5.4

Hi, try to add the --disable-shared flag to your invocation of .configure. Carsten On Mar 22, 2011, at 3:26 PM, Ye MEI wrote: > Thank you for the new version of gromacs. > But the compilation of gromacs failed on my computer. The commands are as > follows: > make distclean > export CC=icc > e

Re: [gmx-users] install problems cygwin

Hi, try to move your files into your cygwin home directory before compiling. If that doesn't work, try to first compile a hello world C program to see why the compiler doesn't work. Roland On Tue, Mar 22, 2011 at 12:13 PM, vijaya subramanian wrote: > > Hi > I am trying to install gromacs on a w

Re: [gmx-users] New maintenance release: gromacs-4.5.4

On Tue, Mar 22, 2011 at 10:26 AM, Ye MEI wrote: > Thank you for the new version of gromacs. > But the compilation of gromacs failed on my computer. The commands are as > follows: > make distclean > export CC=icc > export F77=ifort > export CXX=icc > export CFLAGS="-xS -I/apps/fftw3/include" > exp

[gmx-users] install problems cygwin

Hi I am trying to install gromacs on a windows laptop with rhcygwin. I am doing it as administrator and I ran into the same problem when I tried installing fftw-3.2.2. $ ./configure --enable-sse --enable-float checking for a BSD-compatible install... /usr/bin/install -c checking whether buil

RE: [gmx-users] AFM pulling simulations

too eager to send an email.. I think playing with editconf with princ flag should do the trick .. sorry folks and thanks for the help !! From: xru...@live.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] AFM pulling simulations Date: Tue, 22 Mar 2011 15:47:41 + Thanks Justi

RE: [gmx-users] AFM pulling simulations

Thanks Justin, That is pretty much the only tutorial one can found. I have one question now, how do I force a particular orientation of my protein during genbox (for example if i need to pull along N->C vector, i need my protein oriented that way, i.e in Z direction for example to later appl

Re: [gmx-users] AFM pulling simulations

http://www.gromacs.org/Documentation/Tutorials On 03/22/2011 11:02 AM, X Rules wrote: Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations (constant force/ constant velocity) with gromacs. Can someone point me to a simple tutorial to perform these s

[gmx-users] g_dipole: dipole moment autocorrelation function: Bug?

Hello, I am trying to calculate the non normalized dipole moment autocorrelation function for water. I am using flexible spc water model (define=-DFLEX_SPC). I am using gromacs 4.0.7 version. I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelati

[gmx-users] Re: gmx-users Digest, Vol 83, Issue 153

Message: 4 Date: Tue, 22 Mar 2011 22:26:04 +0800 From: " Ye MEI " Subject: Re: [gmx-users] New maintenance release: gromacs-4.5.4 To: " Discussion list for GROMACS users " Message-ID: <20110326031153...@itcs.ecnu.edu.cn> Content-Type: text/plain; charset="utf-8" Check your error

[gmx-users] Parameterization of a molecule containing a radical (oxygen)

Hi all, I have a question regarding a new parameterization: actually, I'm wondering whether or not it is possible to do it. The molecule is tempol; you cand find its PubChem entry here http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994&loc=ec_rcs As you can see, the problem of this mol

[gmx-users] g_dipole: dipole moment autocorrelation function: Bug?

Hello, I am trying to calculate the non normalized dipole moment autocorrelation function for water. I am using flexible spc water model (define=-DFLEX_SPC). I am using gromacs 4.0.7 version. I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelati

Re: [gmx-users] AFM pulling simulations

X Rules wrote: Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations (constant force/ constant velocity) with gromacs. Can someone point me to a simple tutorial to perform these simulations with gromacs? Thanks, http://www.gromacs.org/Documenta

[gmx-users] AFM pulling simulations

Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations (constant force/ constant velocity) with gromacs. Can someone point me to a simple tutorial to perform these simulations with gromacs? Thanks, -- gmx-us

Re: [gmx-users] New maintenance release: gromacs-4.5.4

Thank you for the new version of gromacs. But the compilation of gromacs failed on my computer. The commands are as follows: make distclean export CC=icc export F77=ifort export CXX=icc export CFLAGS="-xS -I/apps/fftw3/include" export FFLAGS="-xS -I/apps/fftw3/include" export CXXFLAGS="-I/apps/fft

Re: [gmx-users] changing charged groups in CHARMM RNA

thank you for the reply. That settles that. On Tue, Mar 22, 2011 at 2:56 PM, Justin A. Lemkul wrote: > > > maria goranovic wrote: > >> This must be specific to charmm's implementation in gromacs? Out of >> curiosity, why can one not use charge groups ? >> > > http://lists.gromacs.org/pipermail/g

Re: [gmx-users] changing charged groups in CHARMM RNA

maria goranovic wrote: This must be specific to charmm's implementation in gromacs? Out of curiosity, why can one not use charge groups ? http://lists.gromacs.org/pipermail/gmx-users/2010-September/054106.html -Justin On Tue, Mar 22, 2011 at 2:45 PM, Justin A. Lemkul

Re: [gmx-users] changing charged groups in CHARMM RNA

This must be specific to charmm's implementation in gromacs? Out of curiosity, why can one not use charge groups ? On Tue, Mar 22, 2011 at 2:45 PM, Justin A. Lemkul wrote: > > > maria goranovic wrote: > >> Dear List >> >> I was looking at the charged groups in a charmm nucleotide, and could see

Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx

the gro file was the input. I am attaching a pdb as well CRYST1100.0100.0100.0 90.00 90.00 90.00 P 1 1 ATOM 1 P G A 4 5.488 -0.842 0.708 1.00 0.00 P ATOM 2 OP1 G A 4 6.418 0.258 1.047 1.00 0.00 O ATOM 3 OP2 G A 4

Re: [gmx-users] changing charged groups in CHARMM RNA

maria goranovic wrote: Dear List I was looking at the charged groups in a charmm nucleotide, and could see several groups containing 4 to 14 atoms with integer charges. However, the default topology does not have these charged groups. each atom is given a charged group in the default topolo

Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx

maria goranovic wrote: Sorry for the incomplete reply. version 4.5.3, command: pdb2gmx -f guan.pdb -ignh I tried using -ter, but that did not help. It appears that pdb2gmx is not equipped to handle the case of an isolated nucleotide. Keep in mind that pdb2gmx is intended for use with re

Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx

Hi, Is this your input? (a GRO file?). Can you paste the PDB corresponding to the RNA nucleotide that you are interested on? I think the file may be small enough to paste it here so someone can try to reproduce what is happening to you. Daniel 2011/3/22 maria goranovic > Sorry for the incomple

[gmx-users] changing charged groups in CHARMM RNA

Dear List I was looking at the charged groups in a charmm nucleotide, and could see several groups containing 4 to 14 atoms with integer charges. However, the default topology does not have these charged groups. each atom is given a charged group in the default topology. Can we foresee any problem

Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx

Sorry for the incomplete reply. version 4.5.3, command: pdb2gmx -f guan.pdb -ignh I tried using -ter, but that did not help. input coordinate file, pulled out from an RNA molecule. Gromacs Runs On Most of All Computer Systems 34 1GP1 5.549 4.916 5.071 1G OP1

Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx

On 22/03/2011 8:15 PM, maria goranovic wrote: is this a bug of some kind then? someone ? anyone? It's still hard to say. I asked you for your GROMACS version and input coordinate file, and you didn't give us either (in full). While you're there, what pdb2gmx command did you use? Mark just

Re: [gmx-users] Annealing of shell polarizable water model

Ivan Gladich wrote: Dear David Dear all I did the serial run with the same topology and grompp: even if the simulation time is still short (due by the serial run), the temperature profiles are the same (see attached file). As further check, I removed the annealing and the temperature rises

Re: [gmx-users] Annealing of shell polarizable water model

Dear David Dear all I did the serial run with the same topology and grompp: even if the simulation time is still short (due by the serial run), the temperature profiles are the same (see attached file). As further check, I removed the annealing and the temperature rises to 160 K after ~0.5ps

Re: [gmx-users] mdrun the pr.trr

zen...@graduate.org skrev 2011-03-22 10.22: when i type this order :szrun 2 2 mdrun_mpi -nice 0 -v -s pr.tpr -o pr.trr -c b4md.pdb -g pr.log -e pr.edr & the process can not run,and there is a problem that t = 0.000 ps: Water molecule starting at atom 90777 can not be settled. Check for bad co

[gmx-users] New version 4.5.4 of the Gromacs manual

Dear all, The updated version 4.5.4 of the Gromacs manual is available at ftp://ftp.gromacs.org/pub/manual/manual-4.5.4.pdf. Happy simulating! Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.

[gmx-users] mdrun the pr.trr

when i type this order :szrun 2 2 mdrun_mpi -nice 0 -v -s pr.tpr -o pr.trr -c b4md.pdb -g pr.log -e pr.edr & the process can not run,and there is a problem that t = 0.000 ps: Water molecule starting at atom 90777 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb f

Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx

is this a bug of some kind then? someone ? anyone? just bumping, maria On Mon, Mar 21, 2011 at 10:17 AM, maria goranovic wrote: > Here are the contents of my input coordinate file. > > CRYST10.0000.0000.000 90.00 90.00 90.00 P 1 1 > ATOM 1 P G A 4 5.48

Re: [gmx-users] Annealing of shell polarizable water model

Yes, I am running in parallel... Now I will try to run in serial to see if the problem persist Thanks Ivan On 03/22/2011 10:00 AM, David van der Spoel wrote: On 2011-03-22 10.37, Ivan Gladich wrote: Dear all, I would like to heat, very slowly, a ice box of 1796 SWM4-NDP water. This kind of

Re: [gmx-users] Annealing of shell polarizable water model

On 2011-03-22 10.37, Ivan Gladich wrote: Dear all, I would like to heat, very slowly, a ice box of 1796 SWM4-NDP water. This kind of water has 4 sites plus a shell and I am using a small time step (0.1 fms) to heat my ice box from 0 K top 160K in 1 ns. To do that I used a linear annealing from 0

[gmx-users] Annealing of shell polarizable water model

Dear all, I would like to heat, very slowly, a ice box of 1796 SWM4-NDP water. This kind of water has 4 sites plus a shell and I am using a small time step (0.1 fms) to heat my ice box from 0 K top 160K in 1 ns. To do that I used a linear annealing from 0 to 160 K. The simulation run

Re: [gmx-users] checking gen_seed

Alright, thx Mark. From: Mark Abraham To: Discussion list for GROMACS users Sent: Tuesday, March 22, 2011 15:44:51 Subject: Re: [gmx-users] checking gen_seed On 22/03/2011 6:28 PM, Kwee Hong wrote: Hi all, > > >I've accidentally deleted my mdp and .tpr file.

Re: [gmx-users] checking gen_seed

On 22/03/2011 6:28 PM, Kwee Hong wrote: Hi all, I've accidentally deleted my mdp and .tpr file.. :( Is there a way I could check the gen_seed of my simulation from the .tpr or the output of my simulation as I need the info to simulate the same system at another temerature? I don't think gen

[gmx-users] checking gen_seed

Hi all, I've accidentally deleted my mdp and .tpr file.. :( Is there a way I could check the gen_seed of my simulation from the .tpr or the output of my simulation as I need the info to simulate the same system at another temerature? Thanks. Joyce -- gmx-users mailing listgmx-users@gro