Re: [gmx-users] RMSD with Vsite vs No Vsites

well the deviations are about more than 0.5 nm.. On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai wrote: > On 2011-05-05 11:21:54AM -0500, Sikandar Mashayak wrote: > > 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 t

[gmx-users] DO_DSSP

Dear all, I'm trying install do_dssp on my pc.I followed the steps indicated in the page: http://lists.gromacs.org/pipermail/gmx-users/2010-November/055728.html >> 1.step-root at ab-desktop:/path-dsspcmbi.tar.gz/# tar xvzf dsspcmbi.tar.gz >> 2.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp#./D

[gmx-users] NMA problem

Dear All, I am using MM/PBSA to calculate protein-ligand binding affinnity using GROMACS. I got stuck at entropy calculation stage, which can be broadly done by two mthods i.e. Normal Mode Analysis and Quasi-Harmonic method. Can anyone let me know that how minimization using distance based dielec

Re: [gmx-users] RMSD with Vsite vs No Vsites

On 6/05/2011 5:32 PM, Sikandar Mashayak wrote: well the deviations are about more than 0.5 nm.. And what does gmxcheck -s1 -s2 show? Mark On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai > wrote: On 2011-05-05 11:21:54AM -0500, Sikandar Mashayak wrote: > Hi >

Re: [gmx-users] DO_DSSP

On 6/05/2011 5:22 PM, battis...@libero.it wrote: Dear all, I'm trying install do_dssp on my pc. I followed the steps indicated in the page: http://lists.gromacs.org/pipermail/gmx-users/2010-November/055728.html >> 1.step-root at ab-desktop:/path-dsspcmbi.tar.gz/# tar xvzf dsspcmbi.tar.gz

[gmx-users] Nitrate ion

Hi all I need .PDB and .itp file of Nitrate ions. Do any one have them? Thanks alot Best, Maria -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posti

[gmx-users] DO_DSSP

Thank you very much! Anna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www i

Re: [gmx-users] virtual sites

Hi Sikandar A couple of questions regarding the virtual sites. 1) Do I have to number the virtual site in accordance with the atom indices of the rest of the molecule? 2) Is the parameters for the virtual site declared in the atomtypes directive? Cheers Gavin Sikandar Mashayak wrote: > in doin

Re: [gmx-users] virtual sites set up for topology file

Hi I am trying to alter a topology to include 3 virtual sites and I have a few queries, the answers to which are not obvious form the manual. Do I declare the virtual sites in the atomtypes directive like so ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 1

Re: [gmx-users] virtual sites set up for topology file

Hi Having tried to run grompp using the data below I keep getting the following error Fatal error: Unknown vsiten type 7 Does anyone know why this might be? Gavin Gavin Melaugh wrote: > Hi > > I am trying to alter a topology to include 3 virtual sites and I have a > few queries, the answers to wh

Re: [gmx-users] virtual sites set up for topology file

Gavin Melaugh wrote: Hi Having tried to run grompp using the data below I keep getting the following error Fatal error: Unknown vsiten type 7 Does anyone know why this might be? Your [virtual_sites] directive is not correct, either in its name (no such thing as "virtual_sitesn" - the "n" sh

Re: [gmx-users] virtual sites set up for topology file

Hi Justin Thanks for the reply. To create a virtual site at the centre of geometry of 3 atoms, according to the manual, do you not say: [virtual_sitesn], the index of the site, the index of the three atoms and then the function type 1 which determines that it is COG. Or as I now realise. State [vi

Re: [gmx-users] virtual sites set up for topology file

Gavin Melaugh wrote: Hi Justin Thanks for the reply. To create a virtual site at the centre of geometry of 3 atoms, according to the manual, do you not say: [virtual_sitesn], the index of the site, the index of the three atoms and then the function type 1 which determines that it is COG. OK,

Re: [gmx-users] virtual sites set up for topology file

Justin I have tried this but I am now getting different errors. I take it that: I specify the virtual sites in the atomtypes directive as I have seen from examples? I index the virtual sites in the atoms directive in accordance with the rest of the molecule. atom numbers go from 1-228, therefore I

Re: [gmx-users] virtual sites set up for topology file

Gavin Melaugh wrote: Justin I have tried this but I am now getting different errors. I take it that: I specify the virtual sites in the atomtypes directive as I have seen from examples? Virtual sites are included in all the force fields already, but if you want some custom name, then yes, i

Re: [gmx-users] virtual sites set up for topology file

Yeah I see your point about the types. With regard to the initial configuration state I would have assumed that gromacs knew the initial position of the virtual site when I stated that it was to be at the COG of the 3 atoms in the [virtual_sitesn] directive. Justin A. Lemkul wrote: > > > Gavin

Re: [gmx-users] virtual sites set up for topology file

Gavin Melaugh wrote: Yeah I see your point about the types. With regard to the initial configuration state I would have assumed that gromacs knew the initial position of the virtual site when I stated that it was to be at the COG of the 3 atoms in the [virtual_sitesn] directive. I believ

Re: [gmx-users] virtual sites set up for topology file

O.k Cheers Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Yeah I see your point about the types. With regard to the initial >> configuration state I would have assumed that gromacs knew the initial >> position of the virtual site when I stated that it was to be at the >> COG of the 3 atom

Re: [gmx-users] virtual sites set up for topology file

On 6/05/2011 10:17 PM, Gavin Melaugh wrote: Yeah I see your point about the types. With regard to the initial configuration state I would have assumed that gromacs knew the initial position of the virtual site when I stated that it was to be at the COG of the 3 atoms in the [virtual_sitesn] d

Re: [gmx-users] virtual sites set up for topology file

Hi Mark Cheers.Could you perhaps shed some insight into format of [virtual_siten] when trying to define the VS at the COG of three atoms. It is not obvious from the manual Cheers Gavin Mark Abraham wrote: > On 6/05/2011 10:17 PM, Gavin Melaugh wrote: >> Yeah I see your point about the types. Wi

Re: [gmx-users] virtual sites set up for topology file

On 6/05/2011 10:39 PM, Gavin Melaugh wrote: Hi Mark Cheers.Could you perhaps shed some insight into format of [virtual_siten] when trying to define the VS at the COG of three atoms. It is not obvious from the manual Indeed, it's undocumented - but I think Sikander's experience from my discuss

Re: [gmx-users] virtual sites set up for topology file

Mark Abraham wrote: On 6/05/2011 10:39 PM, Gavin Melaugh wrote: Hi Mark Cheers.Could you perhaps shed some insight into format of [virtual_siten] when trying to define the VS at the COG of three atoms. It is not obvious from the manual Indeed, it's undocumented - but I think Sikander's expe

Re: [gmx-users] virtual sites set up for topology file

Hi Mark Many thanks to you and all your colleagues for replying. This has worked, at least there are now no errors. Where the manual is incorrect is that it leads you to believe that you state; [virtual _siten] ;index of VS index of atoms for COG func 229 8 11 15

Re: [gmx-users] virtual sites set up for topology file

Am I correct in saying now, from the following topology (exerpts), that the virtual site VS will only interact with C3? I guess I don't have to give the atom indices of this interaction in the pair list which I use only for 1_4 interactions? Can I use sigma and epsilon in the nonbond_params directi

Re: [gmx-users] trjorder not working

Thanks Justin, that was helpful. I have a following question. Since in my system I have both methanol and water and I want to order both of them ( my eventual aim to make a sphere), is there is way to override -na option ( for water na 4, methanol 3). Is there is way that all the components of th

Re: [gmx-users] trjorder not working

shivangi nangia wrote: Thanks Justin, that was helpful. I have a following question. Since in my system I have both methanol and water and I want to order both of them ( my eventual aim to make a sphere), is there is way to override -na option ( for water na 4, methanol 3). Is there is way

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

Oops, this message and the original should have gone to the VMD mailing list and not Gromacs of course. My mistake, apologies for cluttering your inbox. :-) -Nathan On Thu, May 5, 2011 at 3:35 PM, J. Nathan Scott < scot...@chemistry.montana.edu> wrote: > Hello again, fellow gmx-users, > > I fina

Re: [gmx-users] trjconv center on protein

Dear Justin, Thanks, sure I will give more details. This command I've used for trajectory conversion: trjconv -pbc mol -center -s protein.tpr -f old.trr -o new.trr Then I was analysing a new and old trajectory in VMD with my own script. I have noticed that in old trajectory water234 between fra

Re: [gmx-users] trjconv center on protein

Tomek Wlodarski wrote: Dear Justin, Thanks, sure I will give more details. This command I've used for trajectory conversion: trjconv -pbc mol -center -s protein.tpr -f old.trr -o new.trr Then I was analysing a new and old trajectory in VMD with my own script. I have noticed that in old traj

Re: [gmx-users] virtual sites set up for topology file

Yes, since sigma and epsilon are zero for VS then interactions between and VS-VS and VS-(any other atom) would result in zero force. Since you explicitly define the interaction between VS-C3, combination rule won't be used and C6(VS_C3) and C12(VS_C3) will be computed as per sigma(VS_C3) epsilon(VS

Re: [gmx-users] virtual sites set up for topology file

Cheers Sikandar I take it that because combination rule 3 (provide sigma and epsilon) is stated gromacs assumes that all values in nonbonding parameters are sigma and epsilon. I know this tp be tru for the atomtypes but does it filter down to all intermolecular interactions. Cheers Gavin Sikand

[gmx-users] "No molecules were defined in the system"

Hi all I got .itp and .pdb files of sulfate ion from PRODRG. I add it as an extra molecule (in genbox using -ci) my simulation box. I can see it visaully by VMD in my system. but it is not in topol.top and when I want run my program I receive the following error: "No molecules were defined in the

[gmx-users] Re: "No molecules were defined in the system"

> > I got .itp and .pdb files of sulfate ion from PRODRG. I add it as an extra > molecule (in genbox using -ci) my simulation box. I can see it visaully by > VMD in my system. but it is not in topol.top and when I want run my program > I receive the following error: > > "No molecules were defined i

[gmx-users] The problem of .trr file size limit?

Hello, everyone I submit a job with gromacs-4.5.4 in cluster ,but the md.trr file can not write if the file size more than 17247,252,480K(about 16.06G)? and the program always output :"Cannot write trajectory frame; maybe you are out of quota?" There is sufficient disk space,and the sys

Re: [gmx-users] The problem of .trr file size limit?

The filesystem you're storing on may not allow single files larger than 16.0 GB. What filesystem are you using? ext3? Also, do you really need to write such a large TRR file? Can you store to the TRR file less frequently (for restarts, etc) and store to XTC instead? You'll get *much* more info

Re: [gmx-users] trjconv center on protein

Hey :) Option -center shifts the system, which will show up as a component in the displacement. Cheers, Tsjerk On May 6, 2011 5:39 PM, "Justin A. Lemkul" wrote: Tomek Wlodarski wrote: > > Dear Justin, > > Thanks, sure I will give more details. > > This comman... Are all the measurements being

Re: [gmx-users] virtual sites set up for topology file

yes it will... On Fri, May 6, 2011 at 11:02 AM, Gavin Melaugh wrote: > Cheers Sikandar > > I take it that because combination rule 3 (provide sigma and epsilon) is > stated gromacs assumes that all values in nonbonding parameters are > sigma and epsilon. I know this tp be tru for the atomtypes b

[gmx-users] using tcl to scipt gromacs

I like to use tcl as my scripting language and after much pain and tribulation i have figured out how to get it to call gromacs without raising an error. Use exec -ignorestderr g_yourfavoritegromacsfunction. Note this will only work with versions of tcl 8.5 and later so if you use and older version

[gmx-users] ambar to opls force field

Hello, How can I convert ambar force field to opls force field. Should I half the force constant of bond (Ka) and angle (Kb)? NIlesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/

Re: [gmx-users] ambar to opls force field

Nilesh Dhumal wrote: Hello, How can I convert ambar force field to opls force field. Should I half the force constant of bond (Ka) and angle (Kb)? Why would you do that? Most of the bonded parameters in OPLS were taken from AMBER directly, IIRC. If you need to parameterize some new bon

Re: [gmx-users] ambar to opls force field

On 7/05/2011 8:10 AM, Nilesh Dhumal wrote: Hello, How can I convert ambar force field to opls force field. Should I half the force constant of bond (Ka) and angle (Kb)? Having read the papers describing how their bonded interactions work, shouldn't you know how to convert them? Having a g

[gmx-users] different number of waters (grompp)

Hello dear users, I'm having a problem trying to simulate one trimer. I'm using tip4p water and right after I fill the box with water and try to pre-process (grompp) the resulting .gro and .top, I get the following error: --- Program grompp

Re: [gmx-users] different number of waters (grompp)

Ricardo O. S. Soares wrote: Hello dear users, I'm having a problem trying to simulate one trimer. I'm using tip4p water and right after I fill the box with water and try to pre-process (grompp) the resulting .gro and .top, I get the following error: ---

Re: [gmx-users] different number of waters (grompp)

Justin A. Lemkul wrote: Ricardo O. S. Soares wrote: Hello dear users, I'm having a problem trying to simulate one trimer. I'm using tip4p water and right after I fill the box with water and try to pre-process (grompp) the resulting .gro and .top, I get the following error:

[gmx-users] Using the XTC library

I am trying to use the XTC library in my code but I am just not good at this stuff. http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library I installed using ./configure --prefix=/$HOME/apps/xdrfile make install everything seemed to go well and the make check said everything passed.

Re: [gmx-users] Using the XTC library

On 7/05/2011 1:31 PM, Ryan S Davis (rsdavis1) wrote: I am trying to use the XTC library in my code but I am just not good at this stuff. http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library I installed using ./configure --prefix=/$HOME/apps/xdrfile This might not be the proble

[gmx-users] g_sas query

Hi ALL, I want to calculate the SASA of a protein embedded in a bilayer along with water and ions. So while using g_sas I understand that I need to supply all non-solvent atoms as calculation group and Protein as the output group. So I need to make a group with Protein+Lipid+Ions as the calculatio

Re: [gmx-users] Using the XTC library

You will need to link with the library as well (-lxdrfile) Something like the following should work (if the paths that you provided are correct): icpc -I$HOME/apps/xdrfile/include/xdrfile \ -L$HOME/apps/xdrfile/lib test.cpp -o test -lxdrfile (Since, this is C++ code, then you should be usin

Re: [gmx-users] g_sas query

Hey Anirban, I would consider the ions part of the solvent. But the procedure is right. Cheers, Tsjerk On May 7, 2011 7:35 AM, "Anirban Ghosh" wrote: Hi ALL, I want to calculate the SASA of a protein embedded in a bilayer along with water and ions. So while using g_sas I understand that I ne

Re: [gmx-users] g_sas query

Hello Tsjerk, Thanks for the reply. But if I consider the ions also in the calculation group, then it is not wrong. Right? Thanks, Anirban On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar wrote: > Hey Anirban, > > I would consider the ions part of the solvent. But the procedure is right. > >