Re: [gmx-users] writing trajectory with water molecules within a distance from protein

So, one can probably do this using a simple script? for each frame make index file of water molecules within 0.5 nm using g_select extract frame based on above selection done concatenate frames The only problem with the above would be that the number of water molecules selected might change wit

Re: [gmx-users] writing trajectory with water molecules within a distance from protein

You can use g_order for that with just a bit of additional scripting. Erik maria goranovic skrev 2011-05-10 09.17: So, one can probably do this using a simple script? for each frame make index file of water molecules within 0.5 nm using g_select extract frame based on above selection done co

[gmx-users] reg pdb2gmx

Dear justin , Thanks for your valuable previous reply Also When i run the pdb2gmx tool  i got the following error WARNING: atom O1 is missing in residue PO4 147 in the pdb file WARNING: atom O2 is missing in residue PO4 147 in the pdb file WARNING: atom O3 is missing in residue PO4 147 in the pd

[gmx-users] gromacs make error

dear users while installing gromacs and after running ./configure, i tried to run the "make" command. but soon i was faced with an error witch is typed below. it seems that fftw libraries are not found. i downloaded and installed fftw3.2.2 as mentioned in gromacs website. and put the extracted

[gmx-users] REMD multi core for each replica

Dear GROMACS users, I wonder if it is not possible to use more than 1 core (according to the manual) for each replica using GROMACS 4.0.x? In the manual is written that the number of cores defined by the -np option of mpirun has to be the same as the number of replicas. Thanks Sebastian -- g

Re: [gmx-users] gromacs make error

On 10/05/2011 5:03 PM, Sajad Ahrari wrote: dear users while installing gromacs and after running ./configure, i tried to run the "make" command. but soon i was faced with an error witch is typed below. it seems that fftw libraries are not found. i downloaded and installed fftw3.2.2 as mentione

Re: [gmx-users] reg pdb2gmx

On 10/05/2011 2:31 PM, vidhya sankar wrote: Dear justin , Thanks for your valuable previous reply Also When i run the pdb2gmx tool i got the following error WARNING: atom O1 is missing in residue PO4 147 in the pdb file WARNING: atom O2 is missing in residue PO4 147 in the pdb file WARNING: at

Re: [gmx-users] REMD multi core for each replica

On 10/05/2011 5:36 PM, SebastianWaltz wrote: Dear GROMACS users, I wonder if it is not possible to use more than 1 core (according to the manual) for each replica using GROMACS 4.0.x? You can use more than one core per replica from 4.0 onwards. In the manual is written that the number of co

Re: [gmx-users] writing trajectory with water molecules within a distance from protein

On Mon, May 9, 2011 at 6:28 PM, Mark Abraham wrote: > On 10/05/2011 12:50 AM, maria goranovic wrote: > >> Dear experts >> >> I have a protein simulation in a water box. I now want to write a >> trajectory containing only the protein, and water molecules within 5 >> Angstroms of the protein, with t

Re: [gmx-users] REMD multi core for each replica

Hi Mark, On 05/10/2011 11:34 AM, Mark Abraham wrote: > On 10/05/2011 5:36 PM, SebastianWaltz wrote: >> Dear GROMACS users, >> >> I wonder if it is not possible to use more than 1 core (according to the >> manual) for each replica using GROMACS 4.0.x? > > You can use more than one core per replica

Re: [gmx-users] regarding nacl simulation in water using tabulated potentials

Dear Mark, i followed the same stuff in the tutoriali created the table and tried the following command * grompp -f em.mdp -p tol.top -c nacl3.pdb* i got the following etrrors Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.

Re: [gmx-users] REMD multi core for each replica

On 10/05/2011 7:53 PM, SebastianWaltz wrote: Hi Mark, On 05/10/2011 11:34 AM, Mark Abraham wrote: On 10/05/2011 5:36 PM, SebastianWaltz wrote: Dear GROMACS users, I wonder if it is not possible to use more than 1 core (according to the manual) for each replica using GROMACS 4.0.x? You can

Re: [gmx-users] regarding nacl simulation in water using tabulated potentials

On 10/05/2011 1:04 PM, sreelakshmi ramesh wrote: Dear Mark, i followed the same stuff in the tutoriali created the table and tried the following command * grompp -f em.mdp -p tol.top -c nacl3.pdb* i got the following etrrors Ignoring obsolete mdp entry 'title' Ignoring obsole

[gmx-users] principal moments of ellipsoid

Hi, I want to study the shape change of a macromolecule which seems like a ellipsoid. So, I need obtain the three principal moments of the molecules. Is the command of g_gyrate helpful for me? The sum of the three principal moments should be equal to the . However, I used the command g_gyrate -

Re: [gmx-users] principal moments of ellipsoid

On 10/05/2011 8:23 PM, lammps lammps wrote: Hi, I want to study the shape change of a macromolecule which seems like a ellipsoid. So, I need obtain the three principal moments of the molecules. Is the command of g_gyrate helpful for me? The sum of the three principal moments should be equal t

Re: [gmx-users] writing trajectory with water molecules within a distance from protein

A work around will be available in the future as a plugin for VMD. For your reference read these threads: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/14140.html http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/13217.html On 10 May 2011 03:12, Roland Schulz wrote: > > > O

Re: [gmx-users] principal moments of ellipsoid

Hi, BioVEC is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to berendered as ellipsoids. http://www.phas.ubc.ca/~steve/BioVEC/BioVECindex.html 2011/5/10 Mark Abraham > On 10/05/2011 8:23 PM, lammps lammps wrote: > >> Hi, >> I want to study the

[gmx-users] DFLEXIBLE option

Dear users, I wanted to know when DEFINE = -DFLEXIBLE has to be used. its given in the manual that it has to be used when we require flexible water instead of rigid waters, so if I am using tip4p water model and OPLSAA force field, and i use DFLEXIBLE option in EM and not in position MD, is

Re: [gmx-users] principal moments of ellipsoid

Mark Abraham skrev 2011-05-10 12.31: On 10/05/2011 8:23 PM, lammps lammps wrote: Hi, I want to study the shape change of a macromolecule which seems like a ellipsoid. So, I need obtain the three principal moments of the molecules. Is the command of g_gyrate helpful for me? The sum of the thre

Re: [gmx-users] DFLEXIBLE option

Kavyashree M wrote: Dear users, I wanted to know when DEFINE = -DFLEXIBLE has to be used. its given in the manual that it has to be used when we require flexible water instead of rigid waters, so if I am using tip4p water model and OPLSAA force field, and i use DFLEXIBLE option in EM and

Re: [gmx-users] principal moments of ellipsoid

Not R_x, R_y, and R_z. What I want to obtain are the three three principal moments of the ellipsoidal macromolecule. They are different quantities. 2011/5/10 Erik Marklund > Mark Abraham skrev 2011-05-10 12.31: > > On 10/05/2011 8:23 PM, lammps lammps wrote: >> >>> Hi, >>> I want to study

Re: [gmx-users] principal moments of ellipsoid

lammps lammps wrote: Not R_x, R_y, and R_z. What I want to obtain are the three three principal moments of the ellipsoidal macromolecule. They are different quantities. Then isn't g_principal the more appropriate tool, rather than g_gyrate? -Justin 2011/5/10 Erik Marklund mailt

Re: [gmx-users] DFLEXIBLE option

Thanks With Regards Kavya On Tue, May 10, 2011 at 5:32 PM, Justin A. Lemkul wrote: > > > Kavyashree M wrote: > >> Dear users, >> >> I wanted to know when DEFINE = -DFLEXIBLE has to be used. >> its given in the manual that it has to be used when we require flexible >> water instead of rigid

Re: [gmx-users] principal moments of ellipsoid

Yes, However, what does the data in axis1.dat, axis2.dat, axis3.dat and moi.dat mean? Should I put the center-of-mass of the molecule in the origin when using the g_principal command? It seems that the inertia is calculated relative to the origin. May be my understanding wrong. -- wade -- gmx-

Re: [gmx-users] principal moments of ellipsoid

lammps lammps wrote: Yes, However, what does the data in axis1.dat, axis2.dat, axis3.dat and moi.dat mean? Should I put the center-of-mass of the molecule in the origin when using the g_principal command? It seems that the inertia is calculated relative to the origin. May be my underst

[gmx-users] Re: Fatal error: Atomtype CB not found

Thank you for your informative reply, Sir, Now I understood the problem but when i was tried with another ligand (GSSG) It could be simulated. Later I found error for different ligand. please give me the solution, what sort of force field should be applied? On 9 May 2011 21:27, ITHAYARAJA wr

[gmx-users] Important bugfix for g_hbond

Hi, There have been reports about inconsistencies between older (<= 4.0.7?) and newer versions of g_hbond, where the older seem to have been more reliable. I found and killed the bug that caused the newer versions to miscount the hbonds. Checkout release-4-5-patches to get the bugfix, or patc

Re: [gmx-users] Re: Fatal error: Atomtype CB not found

ITHAYARAJA wrote: Thank you for your informative reply, Sir, Now I understood the problem but when i was tried with another ligand (GSSG) It could be simulated. Later I found error for different ligand. So some systems work and others don't. You haven't described what you're doing, or h

Re: [gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0 SOLVED !

Dear Gromacs user, my intel compiler issue got solved with a combination off autoconfiger and cmake. In a first step, I used autoconfigure for FFTW-3.2.2 and solved my compilation/segfault problems for gromacs-4.5.4 with cmake: ##For FFTW compilation ## ./configure --enable-threads --enable-f

[gmx-users] Changing the pH

Dear GROMACS users, Does someone now how to procede to change the pH of a MD simulation from the physiologic one (7.4) to 6.5 ? Tanos Celmar Costa Franca - D.Sc Coordenador do Programa de Pos-graduacão em Química Secão de Engenharia Química - SE/5 Instituto Militar de Engenharia - IME Rio de

Re: [gmx-users] Changing the pH

Tanos Celmar Costa Franca wrote: Dear GROMACS users, Does someone now how to procede to change the pH of a MD simulation from the physiologic one (7.4) to 6.5 ? Classical MD simulations do not currently allow for dynamic proton exchange. The best you can do at the moment is use pdb2gmx t

[gmx-users] energy group error

Hi All I have set up a topology file and with virtual sites (exerpts below), whereby my virtual sites only interact with the C3 atoms. I am trying to construct a PMF wrt one particular C3. This atom I do not want to interact with the virtual sites at all. I thought the best way to do this was via

Re: [gmx-users] energy group error

Hi again To rephrase. If I have two atoms constructing a charge group, is it not possible to have one of these atoms constructing an energy group on its own? Cheers Gavin Gavin Melaugh wrote: > Hi All > > I have set up a topology file and with virtual sites (exerpts below), > whereby my virtual

[gmx-users] REMD: after replica exchange breakdown

Dear GROMACS User, I'm running a REMD MD of 32 replicas. It worked for the first few replica exchanges. After 30ps again two replicas were exchanged and I received the Error: x particles communicated to PME node y are more than a cell length out of the domain decomposition cell of their charge gro

[gmx-users] charge groups

Hi all Do atoms belonging to the same charge group have to be indexed consecutively in the topology file or can you have the following. [atoms] 1 CA 1 CGECA 1 -0.1150 12.0110 2 CB 1 CGECB 1 0. 12.0110 3 CA

Re: [gmx-users] Changing the pH

Hi Tanos, Perhaps you should try one of the available constant-pH MD methods. Here is a quick explanation of what they do and who is involved in their development right now: http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation My opinion regarding this subject may be a little biase

Re: [gmx-users] energy group error

Gavin Melaugh wrote: Hi again To rephrase. If I have two atoms constructing a charge group, is it not possible to have one of these atoms constructing an energy group on its own? You can't split charge groups, per the error you posted before. -Justin Cheers Gavin Gavin Melaugh wrote: H

Re: [gmx-users] charge groups

Gavin Melaugh wrote: Hi all Do atoms belonging to the same charge group have to be indexed consecutively in the topology file or can you have the following. [atoms] 1 CA 1 CGECA 1 -0.1150 12.0110 2 CB 1 CGECB 1 0.

[gmx-users] g_current and output redirection

I have a pure linux question. When using g_current and trying to redirect its output to the file, e.g. g_current -temp $TEMPER -b $conduct_b -e $conduct_e << EOF >> output 0 EOF only a part of output is written to the file ("output") Here is what is actually written to the file: Selected 0: 'Sy

Re: [gmx-users] charge groups

Hi Justin The two files processed.top and topol.top are the exact same. What is worrying me is that when I look at the topol.tpr from gmxdump, my charge groups do not seem to be specified the way I stated in the topology file. Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi all >>

Re: [gmx-users] g_current and output redirection

Vitaly Chaban wrote: I have a pure linux question. When using g_current and trying to redirect its output to the file, e.g. g_current -temp $TEMPER -b $conduct_b -e $conduct_e << EOF >> output 0 EOF only a part of output is written to the file ("output") Here is what is actually written to t

Re: [gmx-users] charge groups

Gavin Melaugh wrote: Hi Justin The two files processed.top and topol.top are the exact same. What is worrying me is that when I look at the topol.tpr from gmxdump, my charge groups do not seem to be specified the way I stated in the topology file. Can you provide a relevant snippet of the g

Re: [gmx-users] charge groups

As you can see atomnr 7 HC should belong to the same charge group (1) as atomnr 1&2. From the tpr file atomnr 7 (in this file 6) seems to have its own charge group (3). [atoms] ; atomnr type resnr residue namecgnr charge mass 1 CA 1 CGECA 1 -0.1

Re: [gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0 SOLVED !

Hi, Good that managed to solve the issue! Even though it might have been caused by a bug in the autoconf scripts, as these are the final days for the autoconf support in Gromacs, I see a very slim change that it will get investigated/fixed. -- Szilárd On Tue, May 10, 2011 at 4:19 PM, wrote

Re: [gmx-users] charge groups

Gavin Melaugh wrote: As you can see atomnr 7 HC should belong to the same charge group (1) as atomnr 1&2. From the tpr file atomnr 7 (in this file 6) seems to have its own charge group (3). [atoms] ; atomnr type resnr residue namecgnr charge mass 1 CA 1 CGE

Re: [gmx-users] charge groups

O.K cheers I assume that this is irrelevant in vacuum with no cut-offs Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> As you can see atomnr 7 HC should belong to the same charge group (1) as >> atomnr 1&2. From the tpr file atomnr 7 (in this file 6) seems to have >> its own charge gr

Re: [gmx-users] charge groups

Gavin Melaugh wrote: O.K cheers I assume that this is irrelevant in vacuum with no cut-offs Or (for reference) with PME, I would suspect, since in this case charge groups do not have to be net neutral. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: As you can see atomnr

Re: [gmx-users] gromacs make error

Just some hints: - Does the target platform (32/64 bit) or the fftw libs and Gromacs build match? - Try to do a make clean first and (/or?) and reconfigure with --enable-shared. Not sure that it will help, but I vaguely remember something. - Try CMake. Cheers, -- Szilárd On Tue, May 10, 2011

Re: [gmx-users] charge groups

Also. Obviously I arranged the charge groups like this so that they would be neutral, I just didn't realise that the atoms comprising the charge groups had to be in sequence. Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> As you can see atomnr 7 HC should belong to the same charge group (1)

Re: [gmx-users] g_current and output redirection

Thanks, Justin! Great solution. On Tue, May 10, 2011 at 12:57 PM, Justin A. Lemkul wrote: > > > Vitaly Chaban wrote: >> >> I have a pure linux question. When using g_current and trying to >> redirect its output to the file, e.g. >> >> g_current -temp $TEMPER -b $conduct_b -e $conduct_e << EOF >>

[gmx-users] re: simulation-rigid

Hi, I have a protein simulation in which all residues simulate correctly with the exception of five in a loop. These five out of 360 are in a loop (or bend) separate from my area of interest. Thus, I would like to treat them as a rigid sequence. Using the position restraints in the posre.itp

Re: [gmx-users] re: simulation-rigid

Frank Neuhaus wrote: Hi, I have a protein simulation in which all residues simulate correctly with the exception of five in a loop. These five out of 360 are in a loop (or bend) separate from my area of interest. Thus, I would like to treat them as a rigid sequence. Using the position

[gmx-users] Re: [gmx-developers] flexible water model

The gmx-developers list is not the forum for these types of questions. I am replying via gmx-users, which is where the discussion should stay. I took a few minutes to dig into this. My conclusion is that your system is not stable. I would encourage you to analyze the temperature and pressu

[gmx-users] qmmm temp definition

Hi gmxers, I am working on qmmm treatment of a heat shock protein. Heat-sensitive part is treated quantum mechanically, while the other parts classically. I am hence wondering if it is available and applicable in gromacs that this qm part can be heated and cooled for temperature variation purpose

[gmx-users] qmmm linking atom

Hi gmxers, I am just wondering how to give a linking atom's coordinates in a qmmm calculation generally.Would it be normal to take an arithmetic average of two neighboring qmmm-layer-bonding atoms' coordinates? Thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

Re: [gmx-users] qmmm temp definition

On 05/11/2011 08:15 AM, Yao Yao wrote: Hi gmxers, I am working on qmmm treatment of a heat shock protein. Heat-sensitive part is treated quantum mechanically, while the other parts classically. I am hence wondering if it is available and applicable in gromacs that this qm part can be heated

Re: [gmx-users] qmmm linking atom

On 05/11/2011 08:41 AM, Yao Yao wrote: Hi gmxers, I am just wondering how to give a linking atom's coordinates in a qmmm calculation generally. Would it be normal to take an arithmetic average of two neighboring qmmm-layer-bonding atoms' coordinates? Shouldn't this be addressed in the QM-M

Re: [gmx-users] re: simulation-rigid

On 05/11/2011 06:24 AM, Frank Neuhaus wrote: Hi, I have a protein simulation in which all residues simulate correctly with the exception of five in a loop. These five out of 360 are in a loop (or bend) separate from my area of interest. Thus, I would like to treat them as a rigid sequence.

Re: [gmx-users] REMD: after replica exchange breakdown

On 05/11/2011 02:32 AM, SebastianWaltz wrote: Dear GROMACS User, I'm running a REMD MD of 32 replicas. It worked for the first few replica exchanges. After 30ps again two replicas were exchanged and I received the Error: x particles communicated to PME node y are more than a cell length out of t

Re: [gmx-users] energy group error

On 05/11/2011 02:04 AM, Gavin Melaugh wrote: Hi again To rephrase. If I have two atoms constructing a charge group, is it not possible to have one of these atoms constructing an energy group on its own? Correct. Neighbour lists are constructed from the set of whole charge groups in each energ

[gmx-users] Re:qmmm temp definition + linking atom

The link atom can be placed anywhere at step 0. These atom are treated like virtual sites and will thus be placed at the defined position along the QM/MM bond that needs capping. Concerning the temperature, one can treat the QM atoms as a separate group indeed. But as Mark said, why not expo