[gmx-users] gen-pairs

Hi gromacs users, I wish to simulate a system using the Gromos53a6 force field. When I try to run, I get the following errors: ERROR 1 [file topol.top, line 194]: No default LJ-14 types ERROR 2 [file topol.top, line 195]: No default LJ-14 types ERROR 3 [file topol.top, line 198]: No

[gmx-users] using command g_traj to output the trajectory of an ion in the z direction

Hi I am trying to use g_traj to output the trajectory of an ion in the z direction. I used the following command: g_traj_mpi -f cntsol2.trr -s cntsol2.tpr -n cntsol.ndx -z -ox K_nojump.xvg For the option '-z', the manual describes it as 'Plot Z-component'. However, I still got the trajectory

[gmx-users] nrexcl=3

Hi all A very quick question. From the manual the definition of nrexcl =3 is excluding nonbonded interactions between atoms that are no further than 3 bonds away. In say butane does this means that atoms 1 and 4 do not interact, or I take it they interact according to the pair list. Gavin --

Re: [gmx-users] using command g_traj to output the trajectory of an ion in the z direction

toby10222...@sina.com wrote: Hi I am trying to use g_traj to output the trajectory of an ion in the z direction. I used the following command: g_traj_mpi -f cntsol2.trr -s cntsol2.tpr -n cntsol.ndx -z -ox K_nojump.xvg For the option '-z', the manual describes it as 'Plot Z-component'.

[gmx-users] g_order for water

Dear all I am simulating a water slab using a 6-site water model and I would like, for each time step, to calculate the tetrahedrality order parameter of every water oxygens using the four nearest neighbour Oxygens. From g_order documentation I read that this is possible with g_order

[gmx-users] virtual sites

Hi All Is it possible to have a virtual site interact with only specific atoms and not interact at all with everything else? Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] RTP file formats

Hi everyone!   The *.rtp file formats we have on Gromacs rtp file exmaples do not necessarily have the [dihedrals] or [impropers] part. They normally only have the [atoms] and [bonds]. In fact, the [bonds] section do not enumerate the constants or parameters. This is not what is written or

Re: [gmx-users] RTP file formats

Mr Bernard Ramos wrote: Hi everyone! The *.rtp file formats we have on Gromacs rtp file exmaples do not necessarily have the [dihedrals] or [impropers] part. They normally only have the [atoms] and [bonds]. In fact, the [bonds] section do not enumerate the constants or parameters. This is

Re: [gmx-users] RTP file formats

Thanks for the response. We will be using the CHARMM ff. --- On Thu, 5/5/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] RTP file formats To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, May 5, 2011, 8:38

Re: [gmx-users] g_order for water

Dear all, sorry I forgot -Sg option, now it works g_order_d -e 2000 -n index-ow.ndx-Sg By the way I realized that in this way I have only the average of the tetrahedral order parameter inside the group. Is there any possibilities to have the order parameter associated to each oxygen

[gmx-users] trjcat error of different spacing

Hi ALL, I am trying to use trjcat -f input files -o output_file to join to very larger trajectories. However I am getting the following error: --- Continue

Re: [gmx-users] trjcat error of different spacing

Anirban Ghosh wrote: Hi ALL, I am trying to use trjcat -f input files -o output_file to join to very larger trajectories. However I am getting the following error:

Re: [gmx-users] trjcat error of different spacing

Hello Justin, Thanks for the reply. gmxcheck on the first trajectory shows: - Checking file protein_3000NS_2.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 2957280.000 #

Re: [gmx-users] trjcat error of different spacing

Anirban Ghosh wrote: Hello Justin, Thanks for the reply. gmxcheck on the first trajectory shows: - Checking file protein_3000NS_2.trr trn version: GMX_trn_file (single precision) Reading frame

Re: [gmx-users] trjcat error of different spacing

Hello Justin, I am using Gromacs 4.0.7 Actually, I am joining around 20 trajectories of around 300 ns each. Its a CGMD run. But I reported here only those two trajectories between which trjcat has shown the warning while joining. So what should i do? Thanks, Anirban On Thu, May 5, 2011 at 7:58

Re: [gmx-users] trjcat error of different spacing

Anirban Ghosh wrote: Hello Justin, I am using Gromacs 4.0.7 Actually, I am joining around 20 trajectories of around 300 ns each. Its a CGMD run. But I reported here only those two trajectories between which trjcat has shown the warning while joining. So what should i do? Run gmxcheck on

[gmx-users] trjconv problem

Hi, I am having a problem with trjconv to get a single snap-shot from a trajectory file. I am using gromacs 4.0.7 . If I try to get a snapshot corresponding to 14 ps, I was trying to use -b 14 -e 14 command as follows. But, If I issue this command as shown below trjconv --f traj.xtc -o

Re: [gmx-users] trjconv problem

Sanku M wrote: Hi, I am having a problem with trjconv to get a single snap-shot from a trajectory file. I am using gromacs 4.0.7 . If I try to get a snapshot corresponding to 14 ps, I was trying to use -b 14 -e 14 command as follows. But, If I issue this command as shown below trjconv

Re: [gmx-users] trjconv problem

Hi Justin, In many of the frames, if I use -b and -e to be same , it works For example, I found if I use -b 16 -e 16, it gives me the the snapshot at 16ps. But, in many cases like 14ps, it is not working. Also, I tried -b 13 -e 14 -dump 14 . It does not work saying 'WARNING no output,

Re: [gmx-users] virtual sites

yes, you can make virtual sites interact with only specific sites by using Energy Exclusion between energy groups. This can be done by defining energy groups for virtual sites and other atoms, then exclude or include the non-bonded interactions between them accordingly... On Thu, May 5, 2011 at

Re: [gmx-users] virtual sites

Hi Sikandar Cheers. How do you actually define the energy groups? Gavin Sikandar Mashayak wrote: yes, you can make virtual sites interact with only specific sites by using Energy Exclusion between energy groups. This can be done by defining energy groups for virtual sites and other atoms,

Re: [gmx-users] trjconv problem

I found it will work if I use -b 13.9 -e 14.1 From: Sanku M msank...@yahoo.com To: jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, May 5, 2011 10:33:19 AM Subject: Re: [gmx-users] trjconv problem Hi Justin, In many of the

Re: [gmx-users] virtual sites

Gavin Melaugh wrote: Hi Sikandar Cheers. How do you actually define the energy groups? Read in the manual about the .mdp option energygrps and apply custom index groups as necessary. -Justin Gavin Sikandar Mashayak wrote: yes, you can make virtual sites interact with only specific

Re: [gmx-users] virtual sites

you can do it as following 1. create index file make_indx -f conf.gro -n index.ndx ( select VS and any other atoms you want lets say OTHERS) 2. in .mdp define energygrps VS OTHERS 3. exclude interactions by specifying energygrp_excl VS OTHERS in .mdp file for more you can refer to manual.. I

Re: [gmx-users] virtual sites

Hi Justin I am reading the manual at the moment. I want to include some virtual sites in my molecule so that only surrounding CH3s atom type C3 interact with then. All other atoms I don't want to interact with them. Do I create energy groups in the index file called say virtual sites and

[gmx-users] RMSD with Vsite vs No Vsites

Hi As a test case, I did two simulations one the usual Protein in Water and other with Vsites at COM of each monomer but these Vsites dont interact with anyone else. I was expecting results of these two should match almost exactly, but when I compare the rmsd for Protein there seems to be

Re: [gmx-users] virtual sites

Hi Sikandar Many Thanks for the reply. When you define energygrps in the mdp file, does that mean that only these groups are written to the energy file. I take it that all iother information regarding the energy is written as well i.e if you left this section blank Cheers Gavin Sikandar

Re: [gmx-users] virtual sites

Gavin Melaugh wrote: Hi Justin I am reading the manual at the moment. I want to include some virtual sites in my molecule so that only surrounding CH3s atom type C3 interact with then. All other atoms I don't want to interact with them. Do I create energy groups in the index file called say

[gmx-users] Count mismatch for state entry SDx, code count is 754728, file count is 0

Dear Users: Using gromacs 4.0.5, I find that there are at least some cases where some type of disk error can get propagated through both my.tpr and my_prev.tpr, complicating restarts. This used to be a bigger problem in gromacs 3, and I don't recall ever seeing it in gromacs 4 so I thought I

[gmx-users] Re: Count mismatch for state entry SDx, code count is 754728, file count is 0

Apologies: my.tpr and my_prev.tpr should have read my.cpt and my_prev.cpt. On 11-05-05 12:36 PM, Chris Neale wrote: Dear Users: Using gromacs 4.0.5, I find that there are at least some cases where some type of disk error can get propagated through both my.tpr and my_prev.tpr, complicating

Re: [gmx-users] virtual sites

Hi Justin I do not intend to have charges on the sites. All I want is; when a CH3 group gets close to the site it feels a repulsive force. I have calculated a sigma and epsilon value for this interaction. Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I am reading the manual

Re: [gmx-users] virtual sites

hey another approach to do this without using energy group exclusion is to define non-bonded interactions parameter explicitly between atoms in ffnonbonded.itp file. You can specify sigma and epsilon to be zero in virtual sites atoms definition and specify individual pair interactions parameters

Re: [gmx-users] virtual sites

in doing so .. by default all pair interactions with virtual sites would result in zero forces except those between atoms defined in [nonbond_params] On Thu, May 5, 2011 at 11:57 AM, Sikandar Mashayak symasha...@gmail.comwrote: hey another approach to do this without using energy group

[gmx-users] constraints

Hello, In my input file if I don't specify constraints then What is default constraints=none constraints=all bonds NIlesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] constraints

generally, look at mdout.mdp from grompp -- original message -- In my input file if I don't specify constraints then What is default constraints=none constraints=all bonds NIlesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] constraints

Nilesh Dhumal wrote: Hello, In my input file if I don't specify constraints then What is default constraints=none constraints=all bonds See the manual, section 7.3.1 and any relevant section thereafter. Also, read your mdout.mdp file. -Justin --

[gmx-users] serial gromacs on windows

Hey, Could anybody share the executable of gromacs 4.X.X for windows, please? On a related note, if the procedure of compilation is available, why not to put the resulting executable(s) for download? http://www.gromacs.org/Downloads/Installation_Instructions/Windows -- Dr. Vitaly V. Chaban,

Re: [gmx-users] trjorder not working

Hello, Came back to the set of calculations I was doing few days back. I have a box of water (TIP4P), methanol, protein and DHB anions. I minimized this system. Trying to use trjorder for water molecules with respect to the protein (eventually I want to make a sphere by ordering and getting

[gmx-users] Re: Trouble loading User data with a Tcl script (only half the data seems to load)

Hello again, fellow gmx-users, I finally found my coding error that only set the User data for the first half of the frames loaded, it was a simple indexing error after all. However, I would still *greatly* appreciate any assistance with speeding up the following loop: for {set k 6} {$k

Re: [gmx-users] trjorder not working

shivangi nangia wrote: Hello, Came back to the set of calculations I was doing few days back. I have a box of water (TIP4P), methanol, protein and DHB anions. I minimized this system. Trying to use trjorder for water molecules with respect to the protein (eventually I want to make a

[gmx-users] trjconv center on protein

Hi all! I have a trajectory of simulation (protein in box of water) and I would like to have all the time protein in the center of the water box, becasue protein is drifting to the edge during simulation and I am calculating some properties of water arround the protein. I was playing with trjconv

Re: [gmx-users] trjconv center on protein

Tomek Wlodarski wrote: Hi all! I have a trajectory of simulation (protein in box of water) and I would like to have all the time protein in the center of the water box, becasue protein is drifting to the edge during simulation and I am calculating some properties of water arround the protein.

Re: [gmx-users] serial gromacs on windows

On 2011-05-05 03:22:14PM -0500, Vitaly Chaban wrote: Hey, Could anybody share the executable of gromacs 4.X.X for windows, please? On a related note, if the procedure of compilation is available, why not to put the resulting executable(s) for download?

[gmx-users] question regarding g_energy -aver output in gromacs 4.5.4

Dear gmx_users, I have a question regarding the 4.5.4 version of gromacs, and the g_energy program. In the past I had used g_energy with the -aver option, which would give me partial sums along with my instantaneous energy values at each output step. This allowed me to take the difference

Re: [gmx-users] serial gromacs on windows

On Thu, May 5, 2011 at 7:23 PM, Peter C. Lai p...@uab.edu wrote: On 2011-05-05 03:22:14PM -0500, Vitaly Chaban wrote: Hey, Could anybody share the executable of gromacs 4.X.X for windows, please? On a related note, if the procedure of compilation is available, why not to put the

Re: [gmx-users] nrexcl=3

On 5/05/2011 7:41 PM, Gavin Melaugh wrote: Hi all A very quick question. From the manual the definition of nrexcl =3 is excluding nonbonded interactions between atoms that are no further than 3 bonds away. In say butane does this means that atoms 1 and 4 do not interact, or I take it they

Re: [gmx-users] trjconv problem

On 6/05/2011 2:06 AM, Sanku M wrote: I found it will work if I use -b 13.9 -e 14.1 Yes, that is expected. The time for each frame has been computed by adding up the size of each time step stored in a floating-point variable. Such algebra is different from normal algebra - see