[gmx-users] how to specify a location of a molecule in the system

Hello all! I would like to insert a molecule to a membrane system and would like to start from a specific position of the molecule (hydrocarbon or lipid headgroups). I tried doing that in Pymol after converting the merged gro into pdb (using editconf) but when I saved the file in Pymol the order of

Re: [gmx-users] how to specify a location of a molecule in the system

Hi, Perhaps you can do just like you did in pymol, but isntead of saving the file, mearly write down the coordinates of the newborn water and enter it into your gro-file. Cheers, Erik Adva Suez skrev 2010-12-01 08.59: Hello all! I would like to insert a molecule to a membrane system and wo

[gmx-users] Reg: Standard error

Hi Gromacians I am planning to compute the standard error for the interfacial surface tension of water-dichloro ethane. i just want to know is my procedure right. below is the result what i get from my g_energy command. Statistics over 51 steps [ 0. thru 1000.0001 ps ], 1 data sets All av

Re: [gmx-users] Reg: Standard error

On 1/12/2010 7:59 PM, vinothkumar mohanakrishnan wrote: Hi Gromacians I am planning to compute the standard error for the interfacial surface tension of water-dichloro ethane. i just want to know is my procedure right. below is the result what i get from my g_energy command. Statistics over

[gmx-users] Some tools not described any more in online manual

Dear Gromacs-users, Could anyone tell me why some analysis-tools as for example anadock, g_clustsize and others are not described any more in the online-manual? Could that mean that these tools are not supported any more by the Gromacs community or one should not use them because of possible b

Re: [gmx-users] Reg: Standard error

Dear Mark Thank you for your explaination but Its not clear to me what you are trying to say. can you explain it bit more clearly. what should i need to do to get the standard error? any help is highly appreciated. Regards Vinoth On Wed, Dec 1, 2010 at 2:39 PM, Mark Abraham wrote: > On 1/12/201

Re: [gmx-users] Some tools not described any more in online manual

Emanuel Peter wrote: Dear Gromacs-users, Could anyone tell me why some analysis-tools as for example anadock, g_clustsize and others are not described any more in the online-manual? Could that mean that these tools are not supported any more by the Gromacs community or one should not use the

Re: [gmx-users] how to specify a location of a molecule in the system

Adva Suez wrote: Hello all! I would like to insert a molecule to a membrane system and would like to start from a specific position of the molecule (hydrocarbon or lipid headgroups). I tried doing that in Pymol after converting the merged gro into pdb (using editconf) but when I saved the fi

[gmx-users] v-rescale and conserved energy

Dear gromacs users, I am running NVT simulations for polarizable (shell particle) water model (GROMACS version 4.5.1 and 4.5.3 (issue is same in both)) using v-rescale thermostat. While temperature, potential, kinetic and total energies behave quite well I am failing to obtain constant values

[gmx-users] air-water interface

Hi, everyone   I find that i used T and P coupling in water-air interface, that is the reason my system imploded.   So i changed to NVT. But there are still fatal errors.   I have some questions concerning  .gro file.   for example in spc216.gro, there are both + and - psotions. But in other .gro

[gmx-users] Re: gmx-users Digest, Vol 80, Issue 6

Dear All, I have the following error, for both mpi and normal mdrun modes. I tried both using a pull group for the first time, but when the error persisted, went back and used data/md.mdp files which I know work as a test and get the same errors. > > > > [anode27:16555] *** Process received si

RE: [gmx-users] v-rescale and conserved energy

Hi, The integrator is not the issue. The cut-off setup is. You should use interactions that go smoothly to zero with a buffer region in the neighborlist. Use for instance shift for LJ interactions. PME could be switched, but that is a much smaller contribution. Use rlist about 0.3 nm larger th

[gmx-users] Re:Re-installation(4.5.3) mdrun crashes?

Dear All, (this is a repost as I included no subjectline) I have the following error, for both mpi and normal mdrun modes. I tried both using a pull group for the first time, but when the error persisted, went back and used data/md.mdp files which I know work as a test and get the same errors.

Re: [gmx-users] Re:Re-installation(4.5.3) mdrun crashes?

lloyd riggs wrote: Dear All, (this is a repost as I included no subjectline) I have the following error, for both mpi and normal mdrun modes. I tried both using a pull group for the first time, but when the error persisted, went back and used data/md.mdp files which I know work as a test an

Re: [gmx-users] C6 attractive term off OPLSAA

I ran the simulation using a different force field ffG53a6. I modified the ffG53a6nb.itp file by changing the term C6 to zero for nonbonded parameters, but this time for urea in water. The simulation ran fine without any warning or exploding. I don't understand why it would work with one fo

Re: [gmx-users] C6 attractive term off OPLSAA

nishap.pa...@utoronto.ca wrote: I ran the simulation using a different force field ffG53a6. I modified the ffG53a6nb.itp file by changing the term C6 to zero for nonbonded parameters, but this time for urea in water. The simulation ran fine without any warning or exploding. I don't understand

Re: [gmx-users] C6 attractive term off OPLSAA

I see. I actually want to compare my RDFs with C6 term off. Earlier I tried using force.c code file and turned C6 = 0, but when i compared my RDFs, it didn't look any different so I am not sure if it even worked at all or made any difference to the simulation, but again I was using OPLS-AA

Re: [gmx-users] Reg: Standard error

On 1/12/2010 8:25 PM, vinothkumar mohanakrishnan wrote: Dear Mark Thank you for your explaination but Its not clear to me what you are trying to say. can you explain it bit more clearly. what should i need to do to get the standard error? any help is highly appreciated. Like I said, you need

Re: [gmx-users] air-water interface

On 2/12/2010 12:30 AM, 铁锋 彭 wrote: Hi, everyone I find that i used T and P coupling in water-air interface, that is the reason my system imploded. So i changed to NVT. But there are still fatal errors. I have some questions concerning .gro file. for example in spc216.gro, there are both + and

RE: [gmx-users] C6 attractive term off OPLSAA

Hi, Maybe it is not so clear from the topology table in the manual, but when you supply sigma and epsilon as non-bonded parameters, as for OPLS, the nonbond_params section also expects sigma and epsilon. So it seems you could not set only C6 to zero. However there is an, undocumented, trick: if

RE: [gmx-users] C6 attractive term off OPLSAA

I am going to give that a try. Thanks. Quoting Berk Hess : Hi, Maybe it is not so clear from the topology table in the manual, but when you supply sigma and epsilon as non-bonded parameters, as for OPLS, the nonbond_params section also expects sigma and epsilon. So it seems you could not

[gmx-users] Re:Re: Re:RE:Re-installation(4.5.3) mdrun crashes? (Justin A. Lemkul)

Dear All, > If you suspect a faulty installation, then you need to post more > information, like: > > - compilers used > - cmake or autoconf? > - hardware > - commands used to install > > -Justin > > > Sincerely > > > > Stephan Watkins > > Compilers are all standard gnu compilers I used au

[gmx-users] RE:C6 attractive term off OPLSAA

Would I change the sigma to negative in my nb.itp file the way it is set or do I need to include a [nonbond_params] section and make sigma negative in that specific section? because I realize from the manual OPLS-AA uses combination rule 3 but in the manual it shows to combine sigma for i a

[gmx-users] Cut-offs using CHARMM27 ff

Dear Gromacs users, I am trying to use CHARMM27 taking the simulation conditions of two recent articles as guides in optimizing the simulation parameters. (DOI: 10.1021/ct900549r and DOI: 10.1021/jp101581h). -- Both are using PME for electrostatics and I am planning to do that too -- Both ha

[gmx-users] printing a trajectory file in readable format starting from a specific frame other than zero

Hello, Is there a function that allows users to read a trajectory file and print it in a readable format (like gmxdump) but starting from a user- specified frame rather than from 0? Thanks in advance, Silvia Crivelli -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

Re: [gmx-users] printing a trajectory file in readable format starting from a specific frame other than zero

Hi, you can use trjconv to write frames to GRO format. Or you can use it to write a trajectory from a different starting point (and then you can use gmxdump). Roland On Wed, Dec 1, 2010 at 4:39 PM, Silvia Crivelli wrote: > Hello, > > Is there a function that allows users to read a trajectory fi

Re: [gmx-users] Cut-offs using CHARMM27 ff

On Wed, Dec 1, 2010 at 4:30 PM, Hassan Shallal wrote: > Dear Gromacs users, > > I am trying to use CHARMM27 taking the simulation conditions of two recent > articles as guides in optimizing the simulation parameters. *(DOI: > *10.1021/ct900549r > and *DOI:* 10.1021/jp101581h). > > -- Both are u

[gmx-users] virtual sites and heavy atoms for longer time steps

I have some issues to discuss with the mailing list users, 1- Is using virtual sites alone enough to allow me to lengthen the time step from 2 fs to 4 fs, or I have also to use heavy hydrogens when creating topology files in order to use 4 fs time step? 2- Another question, does vitual sites

Re: [gmx-users] virtual sites and heavy atoms for longer time steps

On 2/12/2010 11:13 AM, Hassan Shallal wrote: I have some issues to discuss with the mailing list users, 1- Is using virtual sites alone enough to allow me to lengthen the time step from 2 fs to 4 fs, or I have also to use heavy hydrogens when creating topology files in order to use 4 fs time s

Re: [gmx-users] RE:C6 attractive term off OPLSAA

On 2/12/2010 7:40 AM, nishap.pa...@utoronto.ca wrote: Would I change the sigma to negative in my nb.itp file the way it is set or do I need to include a [nonbond_params] section and make sigma negative in that specific section? because I realize from the manual OPLS-AA uses combination rule 3 b

[gmx-users] Restraining water

Hi, I know it looks a little bit strange, but i was trying to restrain just some water in my system. Now, if i put something like [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 I put restraints on all the molecules. I thought about a tu

[gmx-users] Re: air-water interface

> Hi, everyone > > I find that i used T and P coupling in water-air interface, that is the > reason my system imploded. > > So i changed to NVT. But there are still fatal errors. > > I have some questions concerning  .gro file. > > for example in spc216.gro, there are both + and - psotions. But in

Re: [gmx-users] Restraining water

On 2/12/2010 12:51 PM, Guido Polles wrote: Hi, I know it looks a little bit strange, but i was trying to restrain just some water in my system. Now, if i put something like [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 I put restrai

[gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group"

Dear GMXers, I'm running a simulation of water contact angle measurement on top of graphite surface. Initially a water cubic box is placed on two-layer graphite surface with the rest of the box being vacuum. The water droplet is relaxed during the simulation to develop a spherical shape. An error

Re: [gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group"

On 2/12/2010 4:16 PM, WU Yanbin wrote: Dear GMXers, I'm running a simulation of water contact angle measurement on top of graphite surface. Initially a water cubic box is placed on two-layer graphite surface with the rest of the box being vacuum. The water droplet is relaxed during the simula