Hi,
I have a basic question (since I am new). For starting any simulation as I
understand, is to find a .pdb or .gor file. Pdb files for proteins are
already there, but for a new system what is the easiest and quick way to
find it (which software etc). What about .gro files?
I appreciate yo
attes - http://lattes.cnpq.br/1025157978990218
>
>
> On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed wrote:
>
>> Hi,
>>
>> I have a basic question (since I am new). For starting any simulation as I
>> understand, is to find a .pdb or .gor file. Pdb files for prot
Hi Justin,
On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Hi,
>> Thanks for your comments. But I do not know how to get (or make) the pdb
>> file if it is not made (let say for a new system). Are you using special
>>
Dear all,
I did a simulation of spce water and every thing seemed ok, when I did mdrun
-s file.tpr -o file.trr -c file_out.gro -v -g file.log, I got a file.trr
with zero size, but I have file.xtc that seems fine with VMD. I don't what
happened here. Any idea?
Also I looked at the box size from firs
file.xtc
Thank you,
Jamie
On Wed, Jul 22, 2009 at 11:32 AM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Dear all,
>> I did a simulation of spce water and every thing seemed ok, when I did
>> mdrun -s file.tpr -o file.trr -c file_out.gro -v -g file.log, I got a
>
wn or
double left-hand 'bd-temp' in parameter file"
In file.mdp it is
bd-temp=300
What about this warning related to the problem...??
Thanks,
Jamie
On Wed, Jul 22, 2009 at 11:53 AM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Hi Justin,
>> nstx
Hi,
On Wed, Jul 22, 2009 at 1:13 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Thank you Justin,
>> But how I can prevent from that (filesystem blip) to happen. Also May I
>>
>
> I know nothing about your filesystem, but sometimes these thing
Dear all,
I am simulation spc water system in NVE ensemble. During the grompp stage,
it gave me 2 Notes that rlist should be 0.1-0.3 nm bigger than rcolumb and
rvdw. So I chose rlist=0.9 and two others=0.7 also another Note told me that
I use vdwtye=shift and columbtype=PME-switch. That solved the
Dear gmx users,
Is there a command to convert a *.itp file to a pdb or gro file?? Thanks
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Dear gmx users,
I need some help for generating a itp file for my molecular structure. I am
using molden and now I have the xyz and pdb files. I read through mailing
list but seems I should provide itp myself. But I don't know the right way
to do that. Is it using molden and find one-by-one bond sa
you very much for any suggestion.
On Sat, Aug 8, 2009 at 4:56 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Dear gmx users,
>> I need some help for generating a itp file for my molecular structure. I
>> am using molden and now I have the xyz and pdb
On Sat, Aug 8, 2009 at 5:09 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Hi Justin,
>> I used opls and I already tried PRODRG, but it did not help... I
>>
>
> What force field are you trying to use for your simulation?
>
I am using OPLS.
&
Hi Vitaly,
Actually it doe's not work. I tried but I got error messages for both cases.
Actually the structure is big and contains a c60 part. Do you have any
advice? I could not find in the topology part of archive...
Thanks/Jamie
On Sun, Aug 9, 2009 at 2:54 AM, Vitaly V. Chaban wrote:
> Hi,
ot;25x25x50.itp"
>
>
> [ system ]
> MWCNT with LIBF4 solution
>
>
> [ molecules ]
> 15x15x50 1
> 20x20x50 1
> 25x25x50 1
> LI+ 7
> BF47
> Methanol 254
>
>
>
Hi Justin,
Ok.Thanks for comments and advice, I appreciate.../Jamie
On Mon, Aug 10, 2009 at 3:06 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Dear Vitaly and all,
>> I did copy my top file to a itp file and now for doing a md simulation I
>> ne
SOL 1000
Many Thanks in Advance and I appreciate your help/Jamie
On Mon, Aug 10, 2009 at 5:46 PM, Jamie Seyed wrote:
> Dear Vitaly,
> topol.top: -
> #include "ffoplsaa.itp"
> #include "spce.itp"
> #include "c80ch3.
kul wrote:
>
> Can you post the contents of molecule.itp? The first #include for the
> force field is likely not the problem; you've probably #included it again in
> molecule.itp.
>
> -Justin
>
> Jamie Seyed wrote:
>
>> Dear all,
>> I have a topolo
...??/ Thank you in
advance.../Jamie
On Mon, Aug 10, 2009 at 8:20 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Hi Justin,
>> Oh yes. I had a line that include ff again and I deleted that (is that
>> ok)? now I got a new error related to "number of coordi
First I put 1000, but after editconf and genbox it has been changed to 572.
I only have 1 part with SOL 572...
On Mon, Aug 10, 2009 at 8:36 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Hi Justin,
>> Thanks again... . Actully I have a question: I have 1836 a
Hi Justin,
Is there any information on the gmx-website that explains how I should do
that? Does the tip means I should separate my original structure and the
groups that I attached to it??/ Many Thanks/Jamie
On Mon, Aug 10, 2009 at 9:31 PM, Justin A. Lemkul wrote:
> Jamie Seyed wrote: >
whole
molecule will consider as one group which indeed has a charge=0?? Is this
true??
Thanks a lot/Jamie
On Tue, Aug 11, 2009 at 11:54 AM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Hi Justin,
>> Is there any information on the gmx-website that explains how I
Dear all,
I performed an md simulation but it crashed at the beginning because
according to it "system was exploding". Also when I tried to see the system
by ngmx, there was no water anymore and it was only the molecule sitting in
the box(after grompp and before mdrun it was a box of water plus the
:
> Hi,
>
> On Wed, Aug 12, 2009 at 3:06 AM, Mark Abraham
> wrote:
> > Jamie Seyed wrote:
> >>
> >> Dear all,
> >> I performed an md simulation but it crashed at the beginning because
> >> according to it "system was exploding". Also when
Dear all,
I want to know how can I use genbox to fill inside of the pore as well as a
layer outside. From the "man genbox" page I try to use -shell with a
negative value (?) but it put waters far from the outside of the pore and I
think it does not care about the sign. It seems strange to me becaus
Hi Justin,
Thanks for your answer,
On Thu, Aug 13, 2009 at 11:42 AM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Dear all,
>> I want to know how can I use genbox to fill inside of the pore as well as
>> a layer outside. From the "man genbox" pag
Hi Vitaly,
Thanks for the answer. When I said far away means my pore was in one corner
of vmd window and the water molecules in opposite corner (almost). Anyways,
I tried to use your method but I think I am missing some parts...
I did:
(1)editconf -bt cubic -f conf.gro -o pore_edco.pdb -d 0.02 ---
gt; Jamie Seyed wrote:
>
>> Hi Justin,
>> Thanks for your answer,
>> On Thu, Aug 13, 2009 at 11:42 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Jamie Seyed wrote:
>>
>>Dear all,
>>I want to
V. Chaban wrote:
> What is the box size and what is the cutoff displayed by genbox?
>
> On Thu, Aug 13, 2009 at 8:10 PM, Jamie Seyed wrote:
> > Hi Vitaly,
> > Thanks for the answer. When I said far away means my pore was in one
> corner
> > of vmd window and the water mol
Hi Justin,
Does it mean each time I can add one until I get the number that I want...??
Many Thanks/Jamie
On Thu, Aug 13, 2009 at 2:13 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Hi Justin,
>> I made an insert.gro file for 2 water molecules, and when
. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Hi Justin,
>> Does it mean each time I can add one until I get the number that I
>> want...?? Many Thanks/Jamie
>>
>>
> No need to do it manually. That's what -nmol is for.
>
> -Justin
>
&g
Hi all,
Thanks for your comments. Actually as Vitaly mentioned I am still try to
visualize the gro-file made by genbox. I found out for any number that I use
for "-nmol ? -ci insert.gro" after some iterations and upto these values:
Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45
System total charg
Hi Justin,
Thanks for comments,
On Thu, Aug 13, 2009 at 8:21 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Hi all,
>> Thanks for your comments. Actually as Vitaly mentioned I am still try to
>> visualize the gro-file made by genbox. I found out for any n
Hi Justin,
Thank you very much. I did not know that...
On Thu, Aug 13, 2009 at 8:42 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
> my command is:
>> genbox -cp f.gro -cs spc216.gro -o f_b4em.pdb -p topol.top -shell 0.5
>> -nmol 1 -ci insert.gro
>> I a
Dear all,
I have questions regarding the position restrain md. I tried to find the
answer of my questions from the mailing list, but it is not clear yet.
In the fws tutorial when it says (in the pr.mdp)
tc_grps=Protein non-protein
(1) Doesn't that mean everything in the system? I think for this c
me
know what I am missing here?? Many Thanks in Advance/Jamie
On Fri, Aug 14, 2009 at 8:33 PM, Mark Abraham wrote:
> Jamie Seyed wrote:
>
>> Dear all,
>> I have questions regarding the position restrain md. I tried to find the
>> answer of my questions from the mailing list,
Hi,
How can I make sure that position restraint is actually applied (after
grompp & mdrun)? When I grep "POSRES" or "posres" I can not see any
information... Many Thanks in Advance/Jamie
On Fri, Aug 14, 2009 at 9:07 PM, Mark Abraham wrote:
> Jamie Seyed wrote:
>
the same
order for different systems? Can you please give me some advice about it??
Many Thanks in Advance/ Jamie
On Sat, Aug 15, 2009 at 6:37 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Hi,
>> How can I make sure that position restraint is actually applied
Dear all,
I have a question about groups in index-file. For making an index file for
freezing some atoms, I used procedure like
http://oldwiki.gromacs.org/index.php/g_order and I deleted extra groups. I
added freezegrp and freezedim in my em.mdp and I did em step. Then I jumped
to md step (because
Dear all,
Is there any tool in gromacs that can calculate time correlation
function ??? R(x,y,z). Many Thanks in Advance/Jamie
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20, 2009 at 8:02 PM, Mark Abraham wrote:
> Jamie Seyed wrote:
>
>> Dear all,
>> Is there any tool in gromacs that can calculate time correlation
>> function ??? R(x,y,z). Many Thanks in Advance/Jamie
>>
>
> Yes, various tools can calculate (auto)correlation fun
Hi Mark,
Thanks for the answers. I want to use g_analyze but it needs a file
graph.xvg as an input file. How can I get that for calculation
of auto-correlation function? Many Thanks in Advance/Jamie
On Fri, Aug 21, 2009 at 7:57 PM, Mark Abraham wrote:
> Jamie Seyed wrote:
>
>> Hi Mar
Hi Justin,
Thanks for the answer. I want to calculate auto-correlation function of
R(x,y,z). I mean , .../Many Thanks in Advance/Jamie
On Sat, Aug 22, 2009 at 6:40 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Hi Mark,
>> Thanks for the answers. I want to us
think the average is going to 0 finally (my system is 216 spce water,
20ps). Is this because the simulation time is not long enough?? Many Thanks
in Advance/Jamie
On Sat, Aug 22, 2009 at 6:49 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Hi Justin,
>> Thanks f
not know how to get rid of this error...Thanks in Advance/Jamie
On Sat, Aug 22, 2009 at 8:19 PM, Mark Abraham wrote:
> Justin A. Lemkul wrote:
>
>>
>>
>> Jamie Seyed wrote:
>>
>>> Hi Justin,
>>> Thanks again. I made and used coord.xvg with comma
Hi Justin,
Thanks for the answers. Please check below...
On Sat, Aug 22, 2009 at 9:17 PM, Justin A. Lemkul wrote:
>>
>> On Sat, Aug 22, 2009 at 8:44 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Jamie Seyed wrote:
>>
>>
On Sun, Aug 23, 2009 at 10:30 AM, Jamie Seyed wrote:
> Hi Justin,
> Thanks for the answers. Please check below...
>
> On Sat, Aug 22, 2009 at 9:17 PM, Justin A. Lemkul wrote:
>
>
>>>
>>> On Sat, Aug 22, 2009 at 8:44 PM, Justin A. Lemkul >> jalem...@vt.e
On Sun, Aug 23, 2009 at 7:32 PM, Justin A. Lemkul wrote:
>
>
>
>Actually when I open autocorr.xvg I can see from data/feature
>>extraction/ the last set is S1295 (N=101, autocorr.xvg) which means
>>they are 1296 graphs each with poor statistics start at 1 and coming
>>down. To ha
On Mon, Aug 24, 2009 at 3:44 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
> with a lot of x-y sets seperated by & character. I think I did not get the
>> key point here. So my question is what is the right way to get
>> using this tool?? Many Than
Dear all,
I want to calculate the msd using g_msd. I have a macromolecule and some
(let say 100) water molecules and I want to use msd for water only. from the
manual and list I think I need to make an index for molecules (water) and
use -mol option.
>From David's answer on the list I found
---
n google it only say "g_msd
-n index" and did not explain which index... how about if I use oxygen.ndx
file??
I really appreciate your help. Many Thanks in Advance/Jamie
On Sun, Sep 20, 2009 at 3:33 PM, Mark Abraham wrote:
> Jamie Seyed wrote:
>
>> Dear all,
>> I
cm^2/s
It seems not reasonable to me (negative and its error is bigger than
itself). Any idea?
Thanks in Advance/Jamie
On Sun, Sep 20, 2009 at 7:02 PM, Mark Abraham wrote:
> Jamie Seyed wrote:
>
>> Hi Mark,
>> Thanks for the puzzling answer. I tried the index file counting the
Yes Thanks Justin, should I just use the linear part of msd for fit even if
it is short (like 14ps from 200ps)? Thanks/Jamie
On Sun, Sep 20, 2009 at 8:02 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Thanks Mark,
>> here are the links.
>> http://www.psc
Dear all,
I tried to use g_dipole for a SPC/E water system and I got these results.
-
Dipole moment (Debye)
-
Average = 2.3506 Std. Dev. = 0.0143 Error = 0.0001
The following averages for the complete trajectory have been calculat
Dear Gmx Users,
I have a 2 questions. First about g_velacc and calculating the diffusion
constant from that. In mailing list people say that we need to divide it by
mass squared and 1/3. Then I found another recent post that said it has been
included in the code... Would you please clarify this tha
tion
between them?
Many Thanks in Advance/Jamie
On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Dear Gmx Users,
>> I have a 2 questions. First about g_velacc and calculating the diffusion
>> constant from that. In mailing list peopl
onfiguration
Solvent configuration contains 648 atoms in 216 residues
and then stops
Would you please let me know why it happens?? Many Thanks in Advance/Jamie
On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed wrote:
> Thanks to Justin & Mark for answering my second question...
> Could any
s that you & Mark suggested me to
create a box of water.../Many Thanks/Jamie
On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Dear Gmx users,
>> Does any one know why genbox stops when I use this command:
>> "genbox -cp r
I converted spc216.pdb to gro using editconf. SO they must be the same(?).
The version is 4.0.5 ...it was fine before... yes ran it just now for fws
tuto... how long it takes time in your machine?
On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
Oh, I just changed the [-cs spc216.gro] to [-cp spc216.gro] and this is
working normally...??!! Do you have any idea?
On Sun, Oct 11, 2009 at 1:52 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> I converted spc216.pdb to gro using editconf. SO they must be the
>&
Dear Gmx users,
Does any one know how to convert itp/pdb file to dlpoly FIELD format?? Any
information regarding that will really appreciate... Please let me know if
you have any reference/script ... to make my FIELD file for dlpoly since I
am trying that for a while... Many Thanks in Advance/Jamie
Dear Users,
I am looking for a good reference to find lj parameters for united atoms
representing ACETATE [CH3COO-] and PHOSPHATE [H2PO4-] or [HPO4 2-] groups. I
appreciate if some one guide me in a right direction. Many Thanks in
Advance/Jamie
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